Chemical Information Bulletin
A Publication of the Division of Chemical Information of the ACS
Volume 65 No. 1 (Spring) 2013
Chemical Information Bulletin Vol. 65(1) Spring 2013
David Martinsen, Editor
American Chemical Society
[email protected]
In This Issue
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Message from the Chair
Letter from the Editor
CINF Sponsorship
Reports
 Communications & Publications
 CINF Webinars
 Education Committee
 XCITR
 Book Reviews
 Literature Digest
 Joint Board Council Committee on CAS
 Harry’s Party
Technical Program
 Highlights
 CINFlash
 Committee Meetings and Social Events
 Symposia
 Technical Program Listing
 Technical Program with Abstracts
Awards and Scholarships
Product Announcements
CINF Officers
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20
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25
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123
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133
Cover design by Mark Luchetti
ISSN: 0364-1910
Chemical Information Bulletin, ©Copyright 2013 by the Division of Chemical Information of the American Chemical Society.
(March 19, 2013)
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Message from the Chair
Come April 2013 many chemists will be attending the 245th ACS
National Meeting and Exposition. Will you be there? If so, then
please be sure to check out the very rich program that CINF will
deliver at this meeting. It has been a pleasure to work with the
CINF committees to arrange what we believe is an excellent
opportunity to hear about the exciting work going on in the
domain of chemical information. My hat is off to Rajarshi Guha
and the supporting committees for all of the work they did in
2012 and I can only hope that I can perform the duty of Division
Chair as well as he did. The role of chair is a one year
appointment and, while rather distracted by the work associated
with the two national meetings, it is an opportunity to bring our
personal passions for chemical information to the community. And, I admit, I am full of it...passion
that is...for what CINF can do.
The CINF division has to be one of the most exciting because, let’s be honest, what chemist today is
not using computational tools of some type, is not scouring commercial and public databases for
data or the Internet for information? More than most, our area of chemistry is one that has grown
in importance and impact at an incredible rate. With this in mind I am distressed as to why our
membership has declined rather than grown and I am concerned that despite our best efforts we
are not necessarily addressing the needs of our members and our community-at-large. Based on my
personal experiences over the years we deliver excellent programs at national, regional and local
meetings. At each meeting I attend I am gratified by the camaraderie I feel from my colleagues and
the collective skills, knowledge and wisdom that we are bringing to bear to extend our domain of
practice. That said, as I travel the world meeting chemists, not necessarily chem(o)informaticians
(yes...I AM trying to be all inclusive with both variations of spelling), I am rather surprised that some
chemists only have rudimentary knowledge around basic capabilities such as structure
representation, data exchange, skills in searching for chemical information, etc. Are we failing the
chemistry community by not teaching them and spreading the word about what is feasible today?
While an organic chemist would likely warn me off from attempting many standard syntheses
without a safety net (or at least a fume hood) our domain is different. There is little to lose in trying
things out. There is so much to be discovered, so much value to be gained in attempting to model a
dataset, so many advantages in understanding how to move your data from platform to platform,
from instrument to thesis, from report to online dataset for the world to share in! That said, is any
Internet search a dangerous search? Yes, if you intend to use the information out there as gospel...if
you don’t care whether the hazard warnings are valid, whether the property data are appropriate
and whether the guidance you receive at the end of a query is appropriate to your needs. I say let’s
spread the word and, in parallel, drive our membership higher and participation in our division to
stratospheric levels! If you are a bench chemist and want to learn more about chemical information
and its value to you come and join CINF!
We are at a time of change for how scientists will be measured. The classical measure of a
scientist’s activities and impact is based on where they publish, the impact factors of the journals
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Chemical Information Bulletin Vol. 65(1) Spring 2013
and their citation metrics. But, times are changing, driven by a shift towards more openness in
science as represented by open access publishing, open data and open source code for our
software. Funding agencies are requesting that data associated with their grants are released via
public repositories, open notebook scientists are releasing their data with fully open licensing and
the movement of crowd sourcing that resulted in Wikipedia is fast becoming a part of our domain.
The majority of these areas of science were just starting a few years ago and are already becoming
mainstream. We are in the era of “altmetrics,” some would say new metrics, that measure activities
online, track the value of open data set contributions, measure the “conversation” of scientists as
their contributions traverse the web. We are indeed living in exciting times and CINF can offer an
ideal environment to become immersed in and informed about these movements and the
technologies that both serve and result from these efforts.
In the coming year I intend to encourage our division, our members and the community we support
to come together to offer each other training, materials, platforms and support so that collectively
we can enhance our operating knowledge across the world of chemical information. We will
continue our popular webinars initiated at the end of last year and, if the attendance warrants it,
we can increase their frequency. We want to give a voice to all scientists if your intention is to
educate and stimulate the attendees with travels across the world of chemical information. We will
work to deliver platforms for the management of training materials associated with chemical
information, as was initiated with the XCITR project (www.xcitr.org). You may have additional ideas!
It is, as ever, going to be an exciting year for our division and for chemical information. Please do
attend our online webinars, visit our website, engage with us as members and, should the urge
catch you, become an active volunteer and committee member! Bring your voice to bear on the
issues of today and help us grow the impact of our division to educate, inspire and drive change
across our domain! If you are in New Orleans and have ideas for how CINF can serve you better,
please, let’s talk. If you are a dyed-in-the-wool, been-in-it-from-the-beginning chemical information
professional then I ask you to encourage those early in their careers to join us in CINF as our efforts
will benefit them by having them understand sooner what is possible. Also, let’s reach out across
the divisional lines for collaboration, in programming, and in events, and help mash up the world of
chemistry for the good of all. With that in mind, and paraphrasing a great man, “ask not what your
division can do for you, ask what you can do for your division.” Your participation helps. Sign up,
step up and let’s emphasize the benefits of chemical information!
Dr. Antony J. Williams
Chair, ACS Division of Chemical Information (CINF) @chemconnector
[email protected]
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Letter from the Editor
I would simply like to thank all those who made contributions to this issue of the Chemical
Information Bulletin. Our new division chair, Tony Williams, shared his thoughts on the year
(welcome, Tony!).
Bob Buntrock, our Chief Book Reviewer, submitted two book reviews, both of which follow on from
our recent focus on crime and the macabre in our CINF Luncheons (that doesn’t exactly sound
appetizing). Thanks, Bob, for providing us with some leisurely reading recommendations.
Also included are highlights from the technical program from our Program Chair, Jeremy Garritano,
and a perspective on CINFlash from Rajarshi Guha, as well as the technical program itself. New this
spring is an ePub version of the technical program. This will be available on the CINF website closer
to the National Meeting itself. It will be more mobile-friendly than the PDF version of the CIB.
CAUTION: A special note of caution is appropriate on the Technical Program. In the past, the import
of the Technical Program from ACS into the CIB has been quite labor intensive, and in the
Philadelphia meeting especially, it was not possible to synchronize the last minute changes into the
CIB. This time, the processing of the meeting program is more automated, and should be more
closely aligned with the ACS website. However, the ACS meetings website should still be considered
the most authoritative.
CAUTION: Because people ask, and because I wasn’t aware, I asked Peter Rusch to provide a history
of Harry’s Party. I got everything I wanted to know and more. The entire uncensored PG-13 rated
version has been included. For those who thought the CINF was a staid group of software
developers, cheminformaticians, and librarians (in other words, a bunch of nerds), check it out, but
at your own risk. Note: Unfortunately, Harry’s Party will not be held in New Orleans.
Be sure to check out the product announcements from our sponsors, as well as the information
about submissions for awards. Thanks to Mark Luchetti for the cover page design. Finally, I would
also recognize the efforts of our webmaster, Danielle Dennie, who designed the templates for the
CIB and flowed the content into the system.
Dr. David Martinsen
Guest Editor
Contributors, Volume 65 No.1
The following individuals contributed time or material to this issue of the Chemical Information
Bulletin.
Articles and Features
Guenter Grethe
Rajarshi Guha
Antony Williams
Peter Rusch
Sponsor Information
Graham Douglas
Committee Reports
Grace Baysinger
Jeremy Garritano
Chuck Huber
David Martinsen
Bonnie Lawlor
Technical Program
David Martinsen
Book Reviews
Bob Buntrock
Literature Digest
Song Yu
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Production
David Martinsen, Editor
Danielle Dennie ,Webmaster
Mark Luchetti, Cover Design
Bonnie Lawlor, Copy Editor
Wendy Warr, Copy Editor
Chemical Information Bulletin Vol. 65(1) Spring 2013
Division of Chemical Information Sponsors
Spring 2013
The American Chemical Society Division of Chemical Information is very fortunate to receive
generous financial support from our sponsors to maintain the high quality of the Division’s
programming and to promote communication between members at social functions at the ACS
Spring 2013 National Meeting in New Orleans, LA, and to support other divisional activities during
the year, including scholarships to graduate students in Chemical Information.
The Division gratefully acknowledges contribution from the following sponsors:
Gold
ACS Publications
Bio-Rad Laboratories
Royal Society of Chemistry
Bronze
Accelrys
ACS Style Guide
InfoChem
Journal of Cheminformatics
Optibrium
PerkinElmer
Thieme Chemistry
Opportunities are available to sponsor Division of Chemical Information events, speakers, and
material. Our sponsors are acknowledged on the CINF web site, in the Chemical Information
Bulletin, on printed meeting materials, and at any events for which we use your contribution. For
more information please review the Sponsorship Brochure at http://acscinf.org/PDF/CINF_Not-forprofit_041409.pdf.
Please feel free to contact me if you would like more information about supporting the CINF.
Graham Douglas
Chair, Fundraising Committee
Email: [email protected]
Tel:
510-407-0769
The ACS CINF Division is a non-profit tax-exempt organization with taxpayer ID no. 52-6054220.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Reports: CINF Communications & Publications Committee
CINF Website: A major accomplishment from Communications & Publications is the migration of the
CINF website into a Drupal environment. CINF Webmaster Danielle Dennie, working with an
associate, David Pickup, completed the migration in late February. The new environment will be
much easier to maintain than the previous site. It will even allow non-experts, such as committee
chairs, to add and modify their own web pages. The CIB was moved to the new environment last
year, and Judith Currano and Svetlana Korolev, previous Editors of the CIB, posted some of the
material themselves. Having posted and edited some of the material for this edition, I can also attest
to the relative ease of use of the new environment. Thanks to Danielle and David for a job well
done!
ACS Network: CINF communications are an ongoing concern for the division. Some time ago, we
moved from the CINF Yahoo! groups into the ACS Network. Since then, several issues have arisen.
We have experienced performance issues, usually around the time of the National Meetings.
Unfortunately, this is when we use the system more heavily. Second, there have been several
upgrades to the Network. These have affected navigation, making it difficult to find the appropriate
group. In addition, the default settings for delivery of email when a new message or document has
been posted to a group were changed in one upgrade. To help improve the flow of information for
CINF business, I would to ask CINF Functionaries to check their settings on the ACS Network. If you
are not a member of the ACS Network group, and would like to be, please contact me at
[email protected]. If you are a member, please ensure that you are set to receive notifications
when activity happens in the group. Login at http://communities.acs.org, select “Your Groups”
under the “Your Stuff” at the top of the page. Select the group, in this case “Division of Chemical
Information.” There will be an “Actions” area, and if there is a link to “Stop email notifications,” your
setting is OK. If you see a link to “Receive email notifications,” it means you are not set to get
notified. Click on the link to enable notifications. When you click, the link should change to say “Stop
email notifications.” CINF committee groups are under control of the committee chair, but if you are
in a group, make sure you have the same setting for Action in that group. If you see a link to
“Receive email notifications,” click it to enable notifications.
David Martinsen
Chair, CINF Communications and Publications Committee
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Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Webinars
At the ACS National Meeting in Philadelphia, the Chemical Information Division decided in its Long
Range Planning meeting to experiment with webinars as a way to expand the reach of its
programming beyond the National Meetings. The plan was to begin in 2013, offering a webinar
every 2 months with popular speakers from the symposia. Tony Williams, then Chair-Elect, began
lining up speakers quite quickly, and so the first webinar was held in October, and the second in
December.
Alex Clark, from Molecular Materials, Inc., spoke on “Practical cheminformatics workflows with
mobile apps.” He discussed some of the things he tries to do when
designing apps, and some things to consider when creating apps.
He also discussed some of the drawbacks of tablet computing at
the current time, and the vision he has for creating a fully
functional chemistry environment on mobile devices.
The second webinar saw Jean Claude-Bradley, chemistry professor at Drexel
University, talking about the open science movement. He described his
experience in which students examine the disparity of experimental
measurements in published data, make and post measurements of their own,
and seek to explain why the published values can be so vastly different.
The third webinar featured Jason Priem, graduate
student at the Univerity of North Carolina,
discussing the altmetrics movement. Jason originated the term, which
describes an umbrella of metrics related to article usage and discussion on
articles on social media. These are complementary to impact factor and Hindex. Jason’s webinar was somewhat different from those of the previous
two speakers, both of whom are well known to the CINF community. Jason
has not spoken before at an ACS meeting, but the topic is definitely of interest to CINFers.
The webinars have been hosted using Adobe Connect and MeetingBurner, compliments of ACS
Publications. The first 2 webinars saw between 25 and 40 attendees. The third webinar, of interest
beyond the CINF community, attracted 50 attendees. Webinar information can be found at
http://www.acscinf.org/webinars. Recordings of the webinars can be found at the same address.
David Martinsen
Chair, CINF Communications and Publications Committee
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Report: Education Committee
The Education Committee met on Saturday, August 18, 2012 from 1:00 PM - 3:00 PM, Philadelphia
Convention Center, Room 118A.
Attending:
Chuck Huber, chair, Grace Baysinger, chair 2013-14, Donna Wrublewski, Adrienne Koslowski,
consultant
Review of Philadelphia meeting – August 19 – 23, 2012: The Education Committee was directly
involved with the Thursday afternoon, “Legal, Patent and Digital Rights Management in Publishing”
symposium (Judith Currano presiding; Judith Currano and Chuck Huber, organizers.) The symposia
“Hunting for Hidden Treasures: Chemical Information in Patents and Other Documents” all day
Sunday and “Future of the History of Chemistry” all day Monday were also recommended for their
educational relevance.
Report on Biennial Conference on Chemical Education (BCCE) 2012: Penn State (University Park,
PA) July 29 – August 2, 2012: About 1500 chemical educators attended this year’s meeting. An allday symposium, “Before and After the Lab,” was organized by several Education Committee
members and former members (Grace Baysinger, Judith Currano, Andrea Twiss-Brooks and
Adrienne Koslowski.) It featured nine speakers, a mixture of librarians and chemistry faculty, with
30 attendees at its peak. Presentations included: “Wikipedia in a Writing Assignment,”
“Collaboration Between Faculty and Librarians,” “Presentation Skills for Undergraduates,” “Ethical
Issues,” and “Chemical Information Literacy.” The last, by Grace Baysinger, delved into the CINFendorsed recommendations for chemical information literacy for undergraduates.
Looking ahead to New Orleans – April 7 – 11, 2013: Chemistry of Energy & Food: Symposia of
interest include: “What Chemists Need to Know about IP/Author Rights,” “Food Safety Information”
(organizer: Andrea Twiss-Brooks); “Library Spaces” (organizer: Andrea Twiss-Brooks), and “Public
Chemistry Databases” (organizer: Antony Williams). One symposium, originally slated for New
Orleans, “Print Resources in the Electronic Era” (organizer: Grace Baysinger) has been moved back
to the Indianapolis meeting.
Looking ahead to Indianapolis – September 8 – 12, 2013: Chemistry in Motion: Symposia of
interest include: “Print Resources in the Electronic Era” (see above), “Education for
Cheminformatics” (suggested by the proximity of the Indiana University cheminformatics program;
possible organizer: Jeremy Garritano); “Digital Archiving” (possible organizer: Andrea Twiss-Brooks);
and a student-only session, whether poster or oral to be determined. One symposium slated for
Indianapolis “Chemical Information for Small Teaching Colleges” has been deferred to the San
Francisco Fall 2014 meeting.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Looking ahead to Dallas – March 16 – 20, 2014: The theme for Dallas had not yet been announced.
The committee decided to defer further program planning until the theme is announced.
Looking ahead to BCCE 2014: Grand Valley State University, Annandale, MI, August 3 – 7, 2014:
The theme for this meeting is “Sustainability: Greener on the Grand.” The conference website is:
http://148.61.114.203/bcce/dates.html. The call for workshops begins June 3, 2013; for symposia,
the call begins August 1, 2013. The deadline for both is December 2, 2013. The committee will try to
recruit a local (Michigan-area) liaison for CINF. One complicating factor is how close BCCE 2014 is on
the calendar to the San Francisco ACS National Meeting (the latter begins only a few days after the
former ends.)
Looking ahead to San Francisco – August 10 – 14, 2014: The “Chemical Information for Small
Teaching Colleges” symposium has been deferred to this meeting. As San Francisco meetings are
usually highly attended, we want to prepare more programs once the theme is available.
Information Competencies for Chemistry Undergraduates: Grace Baysinger will add a link to the
current version of the document on the CINF website. We will keep in touch with ACS Committee
on Professional Training to get them to link to the document. The Wikibooks link for the document
is: http://en.wikibooks.org/wiki/Information_Competencies_for_Chemistry_Undergraduates.
Information Competencies for Chemistry Graduates: Judith Currano has prepared an outline.
Grace Baysinger will post a copy of this draft document on ACS Network for the CINF Education
Committee.
Chair-Elect: Selection of a vice-chair/chair-elect was deferred to the New Orleans meeting.
XCITR: All agreed that we need to encourage more of our colleagues to deposit teaching materials
(or links to teaching materials) in XCITR. How best this might be accomplished was not resolved.
Respectively submitted,
Chuck Huber
Chair of CINF Education Committee
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Chemical Information Bulletin Vol. 65(1) Spring 2013
I am delighted to announce that XCITR (Explore Chemical Information Teaching Resources) has
found a new home. After a successful transfer from FIZ Chemie Berlin, the program is now hosted
and maintained by the eScience group of the Royal Society of Chemistry and is accessible at
http://www.xcitr.org.
We are very grateful and thank FIZ Chemie, especially Prof. René Deplanque, Dr. Gregor
Zimmermann and Dr. Ira Fresen, for hosting and maintaining the program in the past. Their efforts
in the development of XCITR are very much appreciated.
The program is a collaborative project of the Division of Computer-Information-Chemistry (CIC) of
the German Chemical Society (GDCh) and the Division of Chemical Information (CINF) of the
American Chemical Society (ACS).
The purpose is to facilitate the availability and distribution of instructional material in chemical
information. XCITR is a hub in which librarians, instructors and information providers deposit and
access important and useful teaching materials. Additionally, one can find educational materials
about library services and collections.
The open source system uses Drupal to make full use of Web 2.0 functionalities. Contents can be
provided as documents (Word, PowerPoint, Excel, and PDF files), embedded videos (from
www.youtube.com) or slideshows (from www.slideshare.net), and as external web-based
instructional materials by providing a link. At present, over 50 documents have been submitted. All
submissions are evaluated by an Editorial Committee to make sure that they are within the scope of
the collection. The system is available at http://www.xcitr.org and can be accessed without a
password for browsing.
We urge readers to become familiar with XCITR and its content and to submit instructional material
that may be of interest and help to other information specialists.
Pull-down menus help make it quick and easy to supply metadata for a resource. When finished,
please choose “Review” on the Workflow tab to initiate the submission process with the editorial
board.
Details of the program and its history are available in the Fall 2011 Newsletter of the Division of
Chemical Education’s Committee on Computers in Chemical Education (CCCE) Newsletter at
http://www.ccce.divched.org/P1Fall2011CCCENL.
Please contact me if you have any questions at [email protected].
Guenter Grethe
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Book Review:
The Scientific Sherlock Holmes: Cracking the Case with Science and Forensics by
James O’Brien, Oxford University Press, New York, 2013. xx + 175 pp. ISBN: 9780-19-979496-6 (hardcover). $29.95.
Along with a review of a book on the history of chemistry, and to some extent forensics, this review
covers a book on chemistry and forensics in literature. Not just any literature, but the famous series
by Sir Arthur Conan Doyle featuring Sherlock Holmes (and Dr. Watson). The Holmes “Canon” is
comprised of sixty stories and all involve some aspect of science. Doyle was the author of other
works besides the Holmes Canon, but the latter is the most famous with many “fan clubs”
worldwide.
In this book, the Canon is described in the Introduction. Chapter one presents a biography of Doyle
who was trained and practiced as a physician. Chapter two presents “biographies” of the main
characters, especially Holmes, Watson, and the arch enemy Moriarty.
Chapter three presents Holmes as a pioneer in forensic science. Poe may have invented the
detective story but Doyle created the forerunner of the modern detective, especially in powers of
deduction. Holmes employs several forensic techniques before they were adopted by distinguished
crime agencies. Included are Bertillon measurements, fingerprints, footprints, handwriting, printed
documents, and cryptology. Application of some of these methods to solving modern, “real” crimes
is described (e.g., the Zodiac Killer and the Lindbergh baby kidnapper).
The book hits its stride in chapter four where Holmes’ expertise in chemistry (he fancied himself as
a chemist) is discussed. Although Watson’s evaluation of Holmes’ chemical expertise evolved over
the course of the stories, Holmes showed his knowledge of coal tar derivatives and dyes, chemical
poisons, and other chemicals. None other than Isaac Asimov criticized Holmes’ chemical expertise,
but O’Brien shows that this criticism was unfounded.
Chapter five covers other sciences and technical issues including math, probability, geometry,
anatomy, botany, physics, optics, astronomy, geology, and meteorology. Chapter six covers ratings
of the Holmes stories, from best to worst. An appendix covers scientific scams that Doyle may or
may not have been involved in, followed by references and an index.
The author, Professor of Chemistry Emeritus at Missouri State University, has previously given a
presentation on Holmes at a symposium at an ACS meeting which was published as an ACS
Symposium Series book1. In addition, on the topic of Holmes and chemistry, the Journal of Chemical
Education announced a virtual online issue titled The Chemical Adventures of Sherlock Holmes.
Whether or not you are a Holmes fan, this book will be an enjoyable read. If you have not read
Holmes previously, you may be induced to read at least some of the stories. If you have read them,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
you may be inspired to read them again with even more enjoyment. The book is also recommended
to those interested in forensic science and the history of chemistry2.
Bob Buntrock
Orono, ME
[email protected]
1. O, Brien, J. F.; Sherlock Holmes: the Eccentric Chemist. In Chemistry and Science Fiction; Stocker,
J. H., Ed.; American Chemical Society: Washington, DC, 1998; pp. 105-125.
2. http://pubs.acs.org/page/jceda8/vi/1
******************
Book Review:
The Case of the Poisonous Socks: Tales from Chemistry by William H. Brock. RSC
Publishing: Cambridge, UK, 2011. vii + 348 pp. ISBN: 978-1-84973-324-3 (paper).
£19.99.
Those who attended the CINF Luncheon at the ACS Meeting in Philadelphia on Aug. 21, 2012, heard
a preview of this book. The author, William Brock, was the speaker and presented several very
entertaining stories about chemists in history. I don’t recall how many of them are in the book, but
he began with the title headliner. Over 150 years of chemical history are covered in forty two
chapters, essays on both chemical topics and the chemists involved. Brock has retired from the
University of Leicester (UK) and has presented these and other essays in journals and magazines as
well as oral presentations. The emphasis is on European chemists, organizations, and education, but
the impact on US chemical history is also presented. The chemists featured range from Justus Liebig
and William Ramsay to C. K. Ingold and C. P. Snow including several women. An excellent, lighter
read, with many stories, both familiar and novel, a great job of fleshing out the personalities of
many chemists in the history of chemistry.
Bob Buntrock
Orono, ME
[email protected]
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Literature Digest
The “Literature Digest” section of the Chemical Information Bulletin is designed to highlight recent
articles by or of interest to the CINF membership. If you have recently authored an article, please tell
us about it! If you have read an article that interested you and that you think would interest others,
we would be delighted to hear about it, as well. Just send us the reference, and we’ll be happy to
review it for inclusion in this column!
The following articles were published since 2012, and were assembled by Song Yu in the month of
March.
Abramo, Giovanni, Ciriaco Andrea D'Angelo, and Flavia Di Costa. 2012. “Identifying
interdisciplinarity through the disciplinary classification of coauthors of scientific
publications.” J. Am. Soc. Inf. Sci. Technol. 63 (11): 2206-2222.
Aguillo, Isidro F. 2012. “Is Google Scholar useful for bibliometrics? A webometric analysis.”
Scientometrics 91 (2): 343-351.
Anon. 2012. “Open access.” Nat. Mater. 11 (5): 353.
Bajorath, Juergen. 2012. “Chemoinformatics: Recent advances at the interfaces between computer
and chemical information sciences, chemistry, and drug discovery.” Bioorg. Med. Chem. 20
(18): 5316.
Bjoerk, Bo-Christer. 2012. “The hybrid model for open access publication of scholarly articles: A
failed experiment?” J. Am. Soc. Inf. Sci. Technol. 63 (8): 1496-1504.
Bornmann, Lutz, Werner Marx, Yuri Gasparyan Armen, and D. Kitas George. 2012. “Diversity, value
and limitations of the journal impact factor and alternative metrics.” Rheumatol Int 32 (7):
1861-7.
Castro, Eduardo A. , and A.K. Haghi. 2012. Advanced methods and applications in chemoinformatics
: research progress and new applications Hershey, PA: Engineering Science Reference.
Enserink, Martin. 2012. “As open access explodes, how to tell the good from the bad and the ugly?”
Science (Washington, DC, U. S.) 338 (6110): 1018.
Franck, Georg. 2012. “Open access: a revolution in scientific publication? Or just a minor
amendment of accessibility?” Cell Cycle 11 (22): 4115-4117.
Giglia, E., and A. Swan. 2012. “Open Access to data for a new, open science.” Eur J Phys Rehabil Med
48 (4): 713-6.
Hambleton, Peter. 2012. “Open access publishing.” Chem. Ind. (Chichester, U. K.) 76 (8): 19.
Harnad, Stevan. 2012. “Open access: A green light for archiving.” Nature (London, U. K.) 487 (7407):
302.
Heller, Stephen, Alan McNaught, Stephen Stein, Dmitrii Tchekhovskoi, and Igor Pletnev. 2013.
“InChI - the worldwide chemical structure identifier standard.” J Cheminform 5 (1): 7.
Jubb, Michael. 2012. “Open access: Let's go for gold.” Nature (London, U. K.) 487 (7407): 302.
Kozak, Marcin, and Lutz Bornmann. 2012. “A new family of cumulative indexes for measuring
scientific performance.” Plos One 7 (10): e47679.
Milojevic, Stasa. 2012. “How are academic age, productivity and collaboration related to citing
behavior of researchers?” Plos One 7 (11): e49176.
Neylon, Cameron. 2012b. “Science publishing: Open access must enable open use.” Nature 492
(7429): 348-9.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Nikolov, Nikolai, Todor Pavlov, R. Niemela Jay, and Ovanes Mekenyan. 2013. “Accessing and using
chemical databases.” Methods Mol Biol 930: 29-52.
Quigley, David, David Freshwater, Mikhail Alnajjar, Dina Siegel, Murty Kuntamukkula, and Fred
Simmons. 2012. “Use of chemical information database accuracy measurements as leading
indicators.” J. Chem. Health Saf. 19 (3): 18-22.
Rordorf, Dietrich. 2012. “Sustained growth of the Impact Factors of MDPI open access journals.”
Molecules 17: 1354-1356.
Smith, Christopher. 2012. “Open access: Hard on lone authors.” Nature (London, U. K.) 487 (7408):
432.
Solomon, David J., and Bo-Christer Bjoerk. 2012a. “Publication fees in open access publishing:
Sources of funding and factors influencing choice of journal.” J. Am. Soc. Inf. Sci. Technol. 63
(1): 98-107.
Solomon, David J., and Bo-Christer Bjoerk. 2012b. “A study of open access journals using article
processing charges.” J. Am. Soc. Inf. Sci. Technol. 63 (8): 1485-1495.
Waltman, Ludo, Clara Calero-Medina, Joost Kosten, Ed C. M. Noyons, Robert J. W. Tijssen, Nees Jan
van Eck, Thed N. van Leeuwen, Anthony F. J. van Raan, Martijn S. Visser, and Paul Wouters.
2012. “The Leiden ranking 2011/2012: Data collection, indicators, and interpretation.” J.
Am. Soc. Inf. Sci. Technol. 63 (12): 2419-2432.
Waltman, Ludo, and Michael Schreiber. 2013. “On the calculation of percentile-based bibliometric
indicators.” J. Am. Soc. Inf. Sci. Technol. 64 (2): 372-379.
Waltman, Ludo, and Nees Jan van Eck. 2012a. “The inconsistency of the h-index.” J. Am. Soc. Inf. Sci.
Technol. 63 (2): 406-415.
Waltman, Ludo, and Nees Jan van Eck. 2012b. “A new methodology for constructing a publicationlevel classification system of science.” J. Am. Soc. Inf. Sci. Technol. 63 (12): 2378-2392.
Waltman, Ludo, Nees Jan van Eck, and Anthony F. J. van Raan. 2012. “Universality of citation
distributions revisited.” J. Am. Soc. Inf. Sci. Technol. 63 (1): 72-77.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
JOINT BOARD-COUNCIL COMMITTEE ON CAS (CCAS) - REPORT TO C&EN
The Committee met in Executive Session on August 17, 2012. CCAS continues to fulfill its
responsibilities in a purposeful manner – serving as a channel for the flow of information between
Society members (and users of CAS services), the ACS Governing Board for Publishing, and CAS
management, assuring that each party’s needs are researched, recognized and represented.
CAS management reported on a number of developments at the most recent meeting, and
members were pleased to learn that new SciFinder training modules have been developed, moving
toward a more integrated, user-focused approach. CAS management has been working with
committee members to seek input on new training approaches to more effectively reach users.
CAS will reach another milestone later this year: The CAS REGISTRY was expected surpass 70 million
organic and inorganic molecules. The Registry maintains its status as the gold standard for
substance information as the largest collection of unique substances.
The “SciFinder Future Leaders in Chemistry” program, established in 2010, again provided an
opportunity for outstanding Ph.D. Chemistry students from around the world to exchange ideas and
experiences in chemistry and informatics. As part of their program experience, they joined
chemistry professionals in Philadelphia to attend the national meeting and exposition.
Members were also pleased to learn that ACS Publications and CAS introduced Reference
QuickView, a dynamic new feature powered by SciFinder that enables readers of web content to
view directly the text of abstracts linked to bibliographic citations within an ACS Publications journal
article or book chapter. Reference QuickView enables readers viewing the full-text HTML version of
an ACS article to scan abstracts from the broader literature, across millions of citations drawn from
a broad array of scientific disciplines covered by CAS.
CCAS continues its role as a conduit of information. The committee communicates its mission
through its web site on the ACS Network where society members as well as nonmembers can post
questions and feedback for CCAS members. Members solicit input from numerous avenues
including local sections, colleges, and patent users. Social media is also being utilized to increase
awareness – a CCAS Facebook has been established.
Reprinted from:
Chemical and Engineering News,
http://cen.acs.org/articles/91/i3/OfficialReports-ACS-National-Meeting.html
Volume 91 Issue 3 | Web Exclusive
Issue Date: January 21, 2013 | Web Date:
January 15, 2013
Submitted by Spiro Alexandratos, CCAS Chair
Notes: Effective January 1, 2013, Grace Baysinger became the Chair of
the Chemical Abstracts Committee. In addition to posting items on
CHMINF-L, CCAS has an open group page on the ACS Network
(https://communities.acs.org/groups/chemical-abstracts-service-committee) and a Facebook page
(https://www.facebook.com/ACSCommitteeChemicalAbstractsService).
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Harry’s Party
By Peter F. Rusch and Harry M. Allcock
“Harry’s Party has been hosted by Harry M. Allcock (IFI/Plenum Data Corporation) at every ACS
National Meeting since the early 1960’s. While ‘unofficial’, it has become a divisional tradition to
which every attendee looks forward on Monday evening.
Every party is well attended and is always considered as the best place to renew old acquaintances,
to make new friends, and to exchange most-up-to-date information, especially on newest trends in
information processing as well as who manages whom and what. The best remembered party was
the one in the Caesars Palace in Las Vegas on August 25, 1980, when Harry and his associates
served drinks standing in a huge decorative bathtub.”
The opening paragraphs are from Val Metanomski’s prodigious and detailed history of the ACS
Division of Chemical Information (CINF). Our objective is to paint a more complete picture filled
with fact, trivia and wit that seemed to pervade all of Harry’s Parties.
Started in 1964 by Harry Allcock (“it’s a title not a name”) when there were few social events for the
Division of Chemical Information at ACS National Meetings, it was a famous meeting place for all
who attended. Generously hosted by Harry until his retirement when FIZ CHEMIE Berlin continued
the tradition until 2012.
Harry headed the successful IFI (Information for Industry) part of Plenum Publishing. Their product
was a series of databases covering US patents for as long a period as data could be found. IFI even
had information that the US Patent and Trademark Office (USPTO) had lost. The databases
contained straightforward bibliographic data for US patents and a deeply indexed portion of high
value.
For those of you who have met Harry, you know he is truly one of the most gregarious people to
ever be in the chemical information business. Can anyone imagine Harry at a National ACS Meeting
and not be involved in a party? Of course not!
Getting the ACS to host a party or, frankly, paying hotel prices for a hosted party, ran counter to
Harry’s sensibilities. So, Harry took things into his own hands. I was a willing accomplice in many of
these, but not at the beginning.
In the early days, Harry and IFI staff would arrange for refreshments, send out the invitations and
have great party. One of Harry’s colleagues, Charlie Merrick, who owned and operated Rapid
Patent, a patent copy service, was always present. Sadly his participation came to an end when he
perished in a helicopter accident while traveling in New Zealand.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Harry continued. Eventually, I (Peter) became involved and it is those parties that I want to share
with you.
How to throw Harry’s Party the old-fashioned way.
Hotel accommodations. Make arrangements at one of the hotels at the ACS National Meeting city,
preferably through some ACS staff member who knows a good party. Reserve a hotel suite with a
bedroom on either side. High floor is good. Arrive at the hotel on Sunday and check-in to the
bedrooms. On Monday (the traditional day for Harry’s Party) get the key to the suite. Open the
doors for inspection.
In Anaheim, Harry was unable to access the bedroom on the other side of the suite. The hotel
manager assured him that the second bedroom would be cleaned and available by the time of the
party. Finally, Harry saw a woman on the balcony that connected the bedrooms and the suite.
Thinking her to be from the housekeeping staff, he politely thanked her for making up the room. In
reality, her business arrangement with the previous occupant was completed and she wasn’t about
to clean up anything.
Refreshments. This starts on Sunday because what’s needed first is several appropriate boxes.
These are easily found at the ACS Exhibition that is setting up. Boxes with corporate logos, such as
Plenum Publishing boxes, are essential. Also go by some booth to acquire a dozen plastic bags.
Mission accomplished and on to phase two.
Harry’s Party is about liquid refreshments. That means: cheap scotch for Harry and other
aficionados, jug (or box) of white wine for those who insist, jug red wine, soft drinks, and beer, lots
of beer. The acquisition varies depending on the likely attendance. As more Germans attended, the
beer component grew. Additionally, napkins, plastic cups, a bag (or maybe 2 bags) of pretzels. All of
this is obtained at a deep-discount liquor store probably (but not always) across town from the
hotel. In New Orleans we walked to and from a drug store on Canal Street in the mid-day heat and
humidity; in Las Vegas it was one of the many cheap liquor stores and a taxi.
Pack all of the stuff in the boxes prior to arrival at the hotel. Hotels don’t want parties to use
outside refreshments. This way, the bell staff will gladly take these boxes of “seminar material” to
the suite and receive a generous tip. Use of suitcases is not recommended (once in Anaheim, a
bottle broke and the leaking suitcase was a dead give-away in the elevator).
Monday afternoon after the announcement is made (vide infra) the next item required is ice. Take
the plastic bags and with the help of one or more accomplices go to every ice machine on all of the
adjacent floors, except the floor where the party will be held. That way the closest ice is the
reserve.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Fill bathtub with ice. Add beer. Set out bags of pretzels and a few napkins. Place IFI sales brochures
next to pretzels. Set up bar. At Caesar’s Palace (vide supra) the bar was the ironing board found in
the room. The bath tub was a Roman tub close to the circular bed with a mirror overhead.
Invitations. On Monday morning go to the CINF session(s) with a note giving the hotel, room
number and time (always 5:00 PM) for Harry’s Party. Have the session chair make announcement.
Believe it or not, there was another “Harry Allcock” who attended most ACS National meetings. He
was known to complain bitterly that his phone rang at all hours with callers asking: “Where’s the
party?” Even though our Harry Allcock always invited him to the party, he vowed to never attend
and never did.
Opening. No directional signs are necessary as by this time everybody knows where Harry’s Party is.
The noise of the gathering crowd is sufficient to direct everyone to the right location. Open the
door. Harry is at the bar to greet everyone and make generous drinks.
Security. Once the party has started it will get crowded. Standing room only is an understatement.
In Caesar’s Palace the heat of the crowd set off the fire alarm prompting a visit from security who
asked that we “keep it down.” In Anaheim, one of the guests started a contest to see if she could
kick the chandelier. She couldn’t so her escort gave it a beefy right hook. In Atlanta, President
Reagan was shot and everyone was on the bed watching TV. In Philadelphia, one of the guests
located a trashy paperback book on an outside balcony on the 23rd floor. It was successfully
retrieved to the delight of the guests. There was no door to the balcony.
Closing. Sooner or later the refreshments are depleted. Even the pretzels are gone. Frankly, not
much is done to keep guests from leaving at 7:00 PM. There’s no more food or drink and they all
have other commitments anyway.
Clean-up. After the guests are gone, put all of the empties and other trash in the plastic bags. In
high-rise hotels there is bank of service elevators usually in a lobby adjacent to the guest elevators.
When the service elevator arrives, look both ways, throw in the bags, push a button for a low floor,
and exit the building by another route.
Repeat.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Technical Program Highlights
ACS Chemical Information Division (CINF)
Spring, 2013 ACS National Meeting
New Orleans, LA (April 6 – 11)
I must start this message by thanking the session organizers and speakers who have committed
themselves to the New Orleans program. Without them, there would not be the wonderful
opportunities to hear about exciting research, network with our peers, or find potential collaborators for
future endeavors. Putting together the program for a National Meeting is not an easy task, and this
being my first attempt, proved to be a challenge. We persevered through the lengthy outage of PACS,
changing deadlines, and other trials to produce a very interesting, diverse, and representative program
for and by our division members as well as inviting outside speakers to complement the sessions. We
have eleven distinct symposia with 124 presentations and other events such as CINFlash, the CINF
Scholarship for Scientific Excellence poster session, and a number of posters being presented at Sci-Mix.
Highlights of the New Orleans program include:
FoodInformatics: Applications of Chemical Information to Food Chemistry
An international line-up of speakers, organized by Jose Medina-Franco and Karina Martinez, is the
division’s contribution to the meeting theme of “Chemistry of Energy and Food.”
Scholarly Communication: New Models, New Media, New Metrics
Changes in scholarly communication are highlighted in this symposium organized by Dave Martinsen, Bill
Town, and Colin Batchelor. Data enhancing publications, citation of data, collaborative research online,
and rewarding contributions in an online environment are some of the subjects that will be discussed.
The day is capped off by a special one-hour presentation from Brian Malow, the self-proclaimed “Earth’s
Premier Science Comedian.” Brian will be discussing communicating science to general audiences. He is
also the CINF Luncheon speaker.
Advances in Visualizing and Analyzing Biomolecular Screening Data
This day and a half symposium, organized by Deepak Bandyopadhyay and Luke Huan, has three subthemes: “Data-Mining Public Bioactivity Data,” “Tools, Techniques, Platforms and Software,” and
“Experimental Insights, Case Studies, and New Methods.”
Library Cafes, Intellectual Commons and Virtual Services, Oh My! Charting New Routes for Users into
Research Libraries
Leah Solla, Teri Vogel and Olivia Bautista Sparks have organized an interesting symposium highlighting
how libraries are adapting physically and virtually to changing patterns of our users. Concepts such as
outreach, scientific computing, changing nature of branch libraries, “open” resources, and
reorganization, provide insight into how research libraries are evolving.
Public Databases Serving the Chemistry Community
Our other day and a half symposium, organized by Tony Williams and Sean Ekins, underscores the
importance of publicly available information. Talks will discuss apps, data quality, linking resources, and
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Chemical Information Bulletin Vol. 65(1) Spring 2013
specific databases and data sets that are freely available. Commercial vendors will also discuss their
efforts in working with the chemistry community and open resources.
Linking Bioinformatic Data and Cheminformatic Data
Ian Bruno and John Overington have organized a daylong session of talks that illustrate the value of
connecting data and information in an increasingly data-saturated environment. Data mining, discovery
engines, profiling/target identification, and data integration/linking are a few of the broader themes of
this symposium.
Advances in Virtual High-Throughput Screening
In this symposium, Joel Freundlich and Sean Ekins have organized talks related to recent techniques that
are improving the screening of potential drug candidates.
Balancing Chemistry on the Head of a Pin: Multi-Parameter Optimization
Ed Champness and Matt Segall have brought together a group of speakers to discuss computational
methods for increased optimization related to drug discovery.
Computational De novo Protein and Peptide Design
Rachelle Bienstock’s session will illuminate recent research related to the design of large molecules.
Food for Thought: Alternative Careers in Chemistry
Donna Wrublewski, Patricia Meindl, and Dana Antonucci have gathered a wide variety of speakers to
discuss different career paths available to those with chemistry backgrounds.
The Program Committee is always looking for ideas, so if you feel that you can contribute, please come
to the CINF program planning meeting on Saturday afternoon at the next conference, or email me,
jgarrita @ purdue.edu, or our incoming Program Chair, David Deng, ddeng @ chemaxon.com, who will
be in charge of organizing the Dallas and San Francisco meetings in 2014.
I hope to see many of you at the Fall Meeting, in Indianapolis. We are already planning a great meeting,
including the Skolnik Award Symposium in honor of Richard Cramer.
Jeremy Garritano
CINF Program Chair
jgarrita @ purdue.edu
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Chemical Information Bulletin Vol. 65(1) Spring 2013
CINFlash - Two Years On
Back in the Fall of 2010 we initiated an experiment of strictly timed, short lightning talks, called
CINFlash. Since then we’ve held this session at every National meeting. A key feature of this
experiment was that it bypassed PACS and the normal abstract submission process. Instead we
accepted abstracts directly by email, right up to a week before the meeting. This was to encourage
submission of recent developments. But more importantly, with little restriction of the range of
topics and the requirement that each talk be 8 minutes long, CINFlash represents a low barrier to
entry opportunity for the chemical information community to get involved in speaking at a National
meeting (though one must already be attending the meeting to present at CINFlash). I think this
aspect could be very useful for students who are attending the meeting as it does not require
preparation of a long talk. More importantly, CINFlash events are intended to be light and fun - of
course, the focus is, as always, on good and interesting science, but the format lends itself to a
degree of levity. So humor is always encouraged!
Given that CINFlash bypasses the official abstract submission system, it only shows up on the official
program as “CINFlash” and does not list any talks. Consequently, it really is a word-of-mouth event,
though we have attempted to spread the word via Twitter, Google+ and other social networks. But
even with this limitation, we have observed a consistent growth in the audience attending as well
as the number of submissions. One of the downsides to the CINFlash format is that the short talk
doesn’t necessarily allow for much discussion, given that we have 8 to 10 talks for each session that
we’ve had. It might be worth it to reduce the number of accepted talks and encourage more
discussion. It’s certainly true that listing talks in the program would encourage better attendance,
but I think it would defeat the purpose of CINFlash - specifically, allowing people to talk about work
that may not have been available 6 months ago (which is how far back the abstract submission
usually closes). The interest in short talks raises the question of whether we should include them in
the official program. One could envisage a session comprised of the usual full length talks, but with
a set of short lightning talks given by speakers who were, say, presenting posters related to the
session topic.
Future tweaks: Currently there is no screening of submissions. I anticipate continued growth of this
session, so in the future we may have to select a subset of submitted talks. Selection of talks may
also be an approach to hosting “focused” flash sessions, where the talks are required to be related
to a pre-defined topic. It would also be useful to encourage speakers scheduled for full talks in
other symposia to consider submitting something for CINFlash. While we currently use social
networks to spread the word about the event, an interesting approach would be to integrate
CINFlash with social networks such as Twitter on the fly - live tweeting from the venue and also
accepting questions from people on Twitter. This would be a good way to get CINF members who
could not make it to the conference to be involved.
But for now CINFlash accepts everybody - if you have something to say about chemical information
or cheminformatics, and can say it in 8 minutes, consider submitting a talk to CINFLash by sending a
(very) short abstract to Rajarsh Guha at [email protected]. And if you’re in New Orleans for the
Spring meeting, consider stopping by the CINFlash session on Sunday between 12:30pm and 2pm in
Room 350 at the Morial Convention Center.
Rajarshi Guha
CINF Flash Organizer and Moderator
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Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Committee Meetings and Social Events
Spring, 2013 ACS National Meeting, New Orleans, LA (April 7-11)
Saturday, April 6
Awards Committee, 1-2pm, Morial Convention Center Room 230
Education Committee, 2-4pm, Morial Convention Center Room 229
Program Committee, 1-4pm, Morial Convention Center Room 231
Executive Committee, 4-6pm, Morial Convention Center Room 229
Functionary Thank-You/Future Brainstorming Dinner, 6:30-9:30pm
Calcasieu Private Dining, 930 Tchoupitoulas St
***Invitation to all Committee members, Session organizers, RSVP to Tony Williams
([email protected])
Sunday, April 7
CSA Trustees, 12-2pm, New Orleans Downtown Marriott at the Convention Center, Tchoupitoulas
Room
Welcoming Reception & Scholarship for Scientific Excellence Posters, 6:30-8:30pm, Morial
Convention Center Room 343
Reception co-sponsored by Bio-Rad Laboratories, InfoChem, Optibrium, PerkinElmer, Thieme
Chemistry, ACS Style Guide and Journal of Cheminformatics.
Scholarships for Scientific Excellence sponsored exclusively by Accelrys.
Sunday, April 7
Symposium: Library Cafes, 8:30 am-5:00pm, Morial Convention Center Room 350
Sponsored by ACS Publications.
Monday, April 8
Division of Chemical Information Featured Presentation, 4:30-5:30pm, Morial Convention Center
Room 352
Brian Malow - “Science comedian's guide to communicating science
Sponsored by the ACS Division of Chemical Information
Tuesday, April 9
CINF Luncheon (Ticketed Event – Contact Division Chair, Tony Williams), 12:00 – 1:30 pm, Morial
Convention Center Room R08
Speaker: Brian Malow - “Science Comedy”
Sponsored exclusively by the Royal Society of Chemistry
23
Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Symposia
ACS Chemical Information Division (CINF)
Spring, 2013 ACS National Meeting
New Orleans, LA (April 7 – 11)
J. Garritano, Program Chair
CINF: Division of Chemical Information
S
M
Advances in Visualizing and Analyzing Biomolecular Screening Data**
D
A
Library Cafes, Intellectual Commons and Virtual Services, Oh My! Charting
New Routes for Users into Research Libraries**
D
CINFlash
P
CINF Scholarship for Scientific Excellence
E
Scholarly Communication: New Models, New Media, New Metrics**
D
Food for Thought: Alternative Careers in Chemistry**
P
FoodInformatics: Applications of Chemical Information to Food Chemistry**
P
Sci-Mix
E
T W T
Linking Bioinformatic Data and Cheminformatic Data
D
Public Databases Serving the Chemistry Community
D
A
Balancing Chemistry on the Head of a Pin: Multi-Parameter Optimization
A
Advances in Virtual High-Throughput Screening
P
Computational De novo Protein and Peptide Design**
P
General Papers
A
Co-sponsored Symposia:
Selecting a co-sponsored symposium will take you outside of the current
Committee, Secretariat or Division
Chairs’ Prime Choices*(COMP)
A
A
Computational Study of Water*(COMP)
D
A
Drug Discovery*(COMP)
D
D
Material Science*(COMP)
P
P
Collaborative Drug Discovery for Neglected Diseases*(COMP)
P
Membranes*(COMP)
D
P
P
Mobile Applications*(COMP)
A
Nanosimulations and Nanoinformatics*(COMP)
P
Poster Session*(COMP)
E
Potential Function Uncertainty and Validation*(COMP)
A
A
A
A
Protein-Ligand Interactions: Insights, New Tools and Applications in Drug
Design*(COMP)
P
D
D
A
Legend:
A = AM, P = PM, D = AM/PM, E = Evening
*Cosponsored symposium with primary organizer shown in parenthesis; located with primary
organizer.
**Primary organizer of cosponsored symposium.
See also: Complete Program
24
Chemical Information Bulletin Vol. 65(1) Spring 2013
Technical Program Listing
ACS Chemical Information Division (CINF)
Spring, 2011 ACS National Meeting
New Orleans, LA (April 7-11)
J. Garritano, Program Chair
[Created Monday, March 18, 2013, Subject to Change]
Sunday, April 7, 2013
10:35 - 5 - Automated structure-activity
relationship mining: Connecting chemical
Advances in Visualizing and Analyzing
structure to biological profiles
Biomolecular Screening Data - AM Session
Mathias Wawer1,
[email protected], David
Data-Mining Public Bioactivity Data
Jaramillo1, Kejie Li1, Sigrun Gustafsdottir1,
Morial Convention Center
Vebjorn Ljosa4, Nicole Bodycombe1, Melissa
Room: 349
Parkin3, Katherine Sokolnicki4, Mark-Anthony
Cosponsored by COMP
Bray4, Ellen Winchester3, George Grant3, Cindy
Deepak Bandyopadhyay, Jun Huan,
Hon1, Jeremy Duvall2, Joshua Bittker2, Vlado
Organizers
Dancik1, Rajiv Narayan5, Aravind
Deepak Bandyopadhyay, Jun Huan, Presiding
Subramanian5, Wendy Winckler3, Todd
8:30 am - 11:50 am
Golub5, Anne Carpenter4, Stuart Schreiber1,
Alykhan Shamji1, Jürgen Bajorath6, Paul
8:30 - Introductory Remarks
Clemons1.
8:35 - 1 - Characterizing the diversity and
biological relevance of the MLPCN assay
manifold and screening set
Jun Huan, [email protected],
11:00 - 6 - Using the bi-clustering SPE for the
visualization and analysis of massive
amounts of compound-target activity data
Dmitrii Rassokhin1, [email protected],
Dimitris Agrafiotis2, Eric Yang2.
9:00 - 2 - New ways to mine disparate
screening data in PubChem
Evan Bolton, [email protected],
11:25 - 7 - BioAssay Research Database: A
platform to support the collection,
management, and analysis of chemical
biology data
Rajarshi Guha1, [email protected], David
Lahr2, Joshua Bittker2, Thomas D.Y. Chung3,
Mark Southern7, Simon Chatwin2, Jeremy J
Yang4, Oleg Ursu4, Christian G Bologa4, Tudor
I Oprea4, Eric Dawson5, Shaun R Stauffer5,
Craig W Lindsley5, Uma Vempati6, Hande
Kucuk6, Stephan C Schurer6, Stephen Brudz2,
Paul A Clemons2, Andrea de Souza2, Noel
Southall1, Dac-Trung Nguyen1, John Braisted1,
Tyler Peryea1.
9:25 - 3 - PubChem DataDicer: A data
warehouse for rapid querying of bioassay
data
Lewis Y Geer, [email protected], Lianyi
Han, Siqian He, Yanli Wang, Evan E Bolton,
Stephen H Bryant.
9:50 - 4 - PubChem widgets
Lianyi Han, [email protected],
10:15 - Intermission
25
Chemical Information Bulletin Vol. 65(1) Spring 2013
Jill E Wilson, [email protected], Leah R
McEwen.
Sunday, April 7, 2013
Library Cafes, Intellectual Commons and
Virtual Services, Oh My! Charting New
Routes for Users into Research Libraries - AM
Session Transforming Libraries
Morial Convention Center
Room: 350
Cosponsored by CHED
11:10 - 14 - Let's work together: ACS
Publications author outreach initiatives and
opportunities for libraries
Sara Rouhi, [email protected],
Sunday, April 7, 2013
Leah Solla, Olivia Bautista Sparks, Teri Vogel,
Organizers
Leah Solla, Teri Vogel, Presiding
8:20 am - 11:45 am
Advances in Visualizing and Analyzing
Biomolecular Screening Data - PM Session
Tools, Techniques, Platforms and Software
Morial Convention Center
Room: 349
Cosponsored by COMP
8:20 - Introductory Remarks
8:25 - 8 - Transformation of academic branch
libraries
Nevenka Zdravkovska, [email protected],
Deepak Bandyopadhyay, Jun Huan,
Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
2:00 pm - 5:15 pm
8:50 - 9 - Library spaces for scientific
computing discovery and learning
Andrea Twiss-Brooks,
[email protected],
2:00 - 15 - 3D phylogenetic trees for
visualization and analysis of complex
datasets
Ruben Abagyan1,2, [email protected],
Eugene Raush2, Maxim Totrov2.
9:15 - 10 - Heart of the university or how to
stay stuck in the middle with you
Susanne J Redalje, [email protected], Lauren
Ray.
2:25 - 16 - On-line graph mining and
visualization of protein-ligand interactome
Clara Ng1, [email protected], Lei
Xie1,2, [email protected].
9:40 - 11 - From traditional library
organization to functional structure: How
does it benefit library users?
Erja Kajosalo, [email protected],
2:50 - 17 - Encoded Library Technology data
analysis: Finding the grain of sand you want
without getting a sunburn
Kenneth E Lind, [email protected], Neil
R Carlson, Ninad V Prabhu, Jeff A Messer.
10:05 - Intermission
10:20 - 12 - Holistic approaches to service:
Connecting researchers to libraries through
relationship building
Kiyomi D. Deards, [email protected],
3:15 - Intermission
3:35 - 18 - Exploring the chemical space of
screening results
Ed Champness, [email protected], Matt
Segall, Chris Leeding, James Chisholm,
Iskander Yusof, Hector Martinez, Nick Foster.
10:45 - 13 - Ask for research alterations:
Emerge with a custom fit
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Chemical Information Bulletin Vol. 65(1) Spring 2013
4:00 - 19 - How to highlight hits: Advances in
visual data analytics tools for HTS data
Jesse A. Gordon,
[email protected], Jess Sager.
for digital documents
Robert E. Belford1, [email protected], Dan
Berleant2, Michael A. Bauer2, Jon L. Holmes3,
John W. Moore3.
4:25 - 20 - Integrated cheminformatics
software for visualizing and analyzing highthroughput screening data
Denis Fourches, [email protected],
Alexander Tropsha.
3:25 - 24 - Navigating scientific resources
using wiki-based resources
Antony J Williams1, [email protected], Valery
Tkachenko1, Alexey Pshenichnov1, Sean Ekins3,
Aileen Day2, Martin Walker4.
4:50 - 21 - Integrating design, analysis, and
visualization into the drug discovery
workflow
W. Patrick P. Walters1,
[email protected], Carlos Faerman1,
Jonathan Weiss1, Xiaodan Zhang1, Roslyn
Potter1, Jun Feng1, Guy Bemis1, Susan
Roberts2, Jason Yuen2, Trevor Kramer2,
Jonathan Christopher3, Jeff Orr3, Brian
Goldman1.
3:50 - 25 - CuLLR me collaboration: Models
and tools for user-driven eLibraries
Dianne Dietrich, [email protected], Leah R
McEwen.
Sunday, April 7, 2013
CINF Scholarship for Scientific Excellence EVE Session
Morial Convention Center
Room: 343
Sunday, April 7, 2013
Guenter Grethe, Organizers
6:30 pm - 8:30 pm
Library Cafes, Intellectual Commons and
Virtual Services, Oh My! Charting New
Routes for Users into Research Libraries - PM
Session Online Tools
Morial Convention Center
Room: 350
Cosponsored by CHED, COMP
26 - iBIOMES: Managing and sharing large
biomolecular simulation datasets in a
distributed environment with iRODS
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3.
27 - Probing the substrate selectivity of the
serotonin and dopamine transporter using
structure based techniques
Amir Seddik1, [email protected],
Harald H. Sitte2, Gerhard F. Ecker1.
Leah Solla, Teri Vogel, Olivia Bautista Sparks,
Organizers
Leah Solla, Teri Vogel, Presiding
2:30 pm - 5:00 pm
2:30 - Introductory Remarks
28 - New cheminformatics microscopes:
Combining semantic web technologies,
cheminformatical representations, and
chemometrics for understanding and
predicting chemical and biological properties
Egon L Willighagen,
[email protected],
2:35 - 22 - Cambridge Structural Database:
Moving with the times
Susan Henderson,
[email protected], Ian J Bruno.
3:00 - 23 - ChemEd DL WikiHyperGlossary: A
social semantic information literacy service
27
Chemical Information Bulletin Vol. 65(1) Spring 2013
29 - Discovery of TLR2 antagonists by virtual
screening
Manuela S Murgueitio1, [email protected], Sandra Santos-Sierra2, Gerhard
Wolber1.
10:10 - 33 - Sharing chemical information
from screens without revealing structures
S. Joshua J. Swamidass1,
[email protected], Matthew Matlock1,
Dimitris K. Agrafiotis2.
Monday, April 8, 2013
10:35 - 34 - Characterization and
visualization of compound combination
responses in a high throughout setting
Rajarshi Guha, [email protected], Lesley
Mathews, John Keller, Paul Shinn, Craig
Thomas, Anton Simeonov, Marc Ferrar.
Advances in Visualizing and Analyzing
Biomolecular Screening Data - AM Session
Experimental Insights, Case Studies, and
New Methods
Morial Convention Center
Room: 349
Cosponsored by COMP
11:00 - 35 - Characterizing activity
landscapes using network-like similarity
graphs to mine antibacterial data
Veerabahu Shanmugasundaram1,
[email protected],
Steven Heck1, Justin Montgomery1, Preeti
Iyer2, Dilyana Dimova2, Jürgen Bajorath2.
Deepak Bandyopadhyay, Jun Huan,
Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
8:30 am - 11:55 am
8:30 - Introductory Remarks
11:25 - 36 - From hits to leads: Data
visualization of chemical scaffolds beyond
traditional SAR exploration
Tyler Peryea, [email protected], John
Braisted, Ajit Jadhav, Rajarshi Guha, Noel
Southall, Dac-Trung Nguyen.
8:35 - 30 - Dispensing processes profoundly
impact biological assays and computational
and statistical analyses
Sean Ekins1, [email protected], Joe
Olechno2, Antony J Williams3.
11:50 - Concluding Remarks
9:00 - 31 - On the compound annotation and
cleaning the GSK screening collection
initiative: The utility of an Inhibition
Frequency Index (IFI)
Subhas J Chakravorty,
[email protected], James A
Chan, Juan Luengo, Nicole M Greenwood,
Ioana Popa-Burke, Ricardo Macarron.
Monday, April 8, 2013
Scholarly Communication: New Models, New
Media, New Metrics - AM Session
Morial Convention Center
Room: 350
David Martinsen, William Town, Colin
Batchelor, Organizers
David Martinsen, Presiding
8:10 am - 11:30 am
9:25 - 32 - Analyzing screening and similarity
searching outcome in light of multiple
approaches to the same target
Tina Garyantes, [email protected],
8:10 - Introductory Remarks
9:50 - Intermission
8:15 - 37 - Evolution of ACS DivCHED CCCE
ConfChem: Gopher servers to the social
28
Chemical Information Bulletin Vol. 65(1) Spring 2013
semantic web
Robert E Belford1, [email protected], Nitin
Agarwal2, Steven Leimberg2, Jon L. Holmes3.
education
Gerhard Klimeck, [email protected],
Monday, April 8, 2013
8:45 - 38 - Data enhancing the RSC Archive
Colin Batchelor1, [email protected], Ken
Karapetyan2, Alexey Pshenichnov2, David
Sharpe1, Jon Steele1, Valery Tkachenko2,
Antony Williams2.
FoodInformatics: Applications of Chemical
Information to Food Chemistry - PM Session
Morial Convention Center
Room: 349
Cosponsored by AGFD
9:15 - 39 - NIST-journal cooperation to
improve the quality of published
experimental data: Pre-acceptance
evaluation and on-line tools
Robert D. Chirico1, [email protected],
Michael Frenkel1, Joseph W. Magee1, Vladimir
V. Diky1, Kenneth Kroenlein1, Chris D. Muzny1,
Andrei F. Kazakov1, Ilmutdin M. Abdulagatov1,
Gary R. Hardin1, Theodoor W. de Loos2, John
P. O'Connell3, Clare McCabe4, Joan F.
Brennecke5, Paul M. Mathias6, Anthony R. H.
Goodwin7, Jiangtao Wu8, Kenneth N. Marsh9,
Ronald D. Weir10, William E. Acree, Jr.11, Agilio
Pádua12, W. M. (Mickey) Haynes1, Daniel G.
Friend1, Andreas Mandelis13, Vicente Rives14,
Christoph Schick15, Sergey Vyazovkin16, Ella
Chen17.
Jose Medina-Franco, Karina Martinez
Mayorga, Organizers
Jose Medina-Franco, Presiding
1:30 pm - 5:30 pm
1:30 - Introductory Remarks
1:35 - 43 - Soft and fuzzy approach to food
informatics
Gerald M Maggiora,
[email protected],
2:00 - 44 - Exploring the chemical space of
flavors and fragrances with the chemical
universe database
Jean-Louis Reymond1, [email protected], Lars Ruddigkeit1,
Mahendra Awale1, Guillaume Godin2.
9:45 - Intermission
2:25 - 45 - Tracing pharmacophore
determinants of natural- and nutritional-like
components in epigenetics and metabolism
Alberto Del Rio, [email protected],
10:00 - 40 - Reproducibility in
cheminformatics and computational
chemistry research: Certainly we can do
better than this
Gregory A. Landrum,
[email protected],
2:50 - 46 - Reverse pharmacognosy: From
molecules to active ingredients
Quoc Tuan Do,
[email protected], Sylvain
Blondeau, Philippe Bernard.
10:30 - 41 - Reproducible research applied to
cheminformatics experiments
Paul J Kowalczyk,
[email protected],
3:15 - 47 - Flavor network: Exploring the
principles of food pairing
Sebastian E Ahnert1, [email protected],
Yong-Yeol Ahn2, Albert-Laszlo Barabasi3.
11:00 - 42 - Mythbusting scientific
knowledge transfer with nanoHUB.org:
Collaborative research and dissemination
with quantifiable impact on research and
29
Chemical Information Bulletin Vol. 65(1) Spring 2013
recommendations
David P Martinsen, [email protected],
3:40 - Intermission
3:50 - 48 - USP reference standards as valueadded information sources in the Food
Chemicals Codex (FCC)
Christina L. Cole, [email protected],
1:35 - 53 - Digital research that is
discoverable, citable, and linked to primary
research literature: The Data Citation Index
Daphne Grecchi,
[email protected],
4:15 - 49 - Reaxys as an information resource
for food chemistry
David Evans1, [email protected],
Juergen Swienty-Busch2.
2:05 - 54 - From inception to collaboration to
publication: A complete integrated research
management platform for researchers
Judy Chen, [email protected],
4:40 - 50 - Profiling the trace metal
composition of wine as a function of storage
temperature and packaging type
Helene Hopfer1,2, [email protected],
Jenny Nelson3, Carolyn L Doyle1,2, Hildegarde
Heymann1, Alyson E. Mitchell2,4, Susan E.
Ebeler1,2.
2:35 - Intermission
2:50 - 55 - Evolving with our community: The
RSC's approach to the challenges and
opportunities of scientific communication
Richard Kidd, [email protected], James Milne.
5:05 - 51 - Mining the protein space to
determine prevalence of fragments identical
with allergenic epitopes - chicken egg
protein fragments as an example
Piotr Minkiewicz, [email protected],
Monika Protasiewicz, Małgorzata Darewicz,
Karolina Hurman, Anna Iwaniak.
3:20 - 56 - We're not in Kansas anymore
Roger Schenck, [email protected],
3:50 - 57 - Challenging, cajoling, and
rewarding the community for their
contributions to online chemistry
Antony J Williams1, [email protected],
Valery Tkachenko1, Alexey Pshenichnov1, Will
Russell2, Jack Rumble2, David Leeming2.
Monday, April 8, 2013
Scholarly Communication: New Models, New
Media, New Metrics - PM Session
Morial Convention Center
Room: 352
Cosponsored by YCC
4:20 - Intermission
4:30 - 58 - Science comedian's guide to
communicating science to general audiences
Brian Malow,
[email protected],
William Town, Colin Batchelor, David
Martinsen, Organizers
Colin Batchelor, William Town, Presiding
1:00 pm - 5:30 pm
Monday, April 8, 2013
Food for Thought: Alternative Careers in
Chemistry - PM Session
Morial Convention Center
Room: 350
Cosponsored by PROF, YCC
1:00 - Introductory Remarks
1:05 - 52 - Supplementary journal article
materials: Summary of the NISO/NFAIS
30
Chemical Information Bulletin Vol. 65(1) Spring 2013
Donna Wrublewski, Patricia Meindl,
Organizers
Patricia Meindl, Presiding
1:15 pm - 5:15 pm
Sci-Mix - EVE Session
Morial Convention Center
Room: Hall D
Jeremy Garritano, Organizers
8:00 pm - 10:00 pm
1:15 - Introductory Remarks
1:20 - 59 - From studying block copolymers
to chemical information: A journey of an
alternative chemistry career as an academic
science librarian
Vincent F Scalfani, [email protected],
1 - Characterizing the diversity and biological
relevance of the MLPCN assay manifold and
screening set
Jun Huan, [email protected],
4 - PubChem widgets
Lianyi Han, [email protected],
1:50 - 60 - Successful careers in science: Why
moving away from the bench brings you
closer to advancing research
Lily Khidr, [email protected],
6 WITHDRAWN
16 - On-line graph mining and visualization
of protein-ligand interactome
Clara Ng1, [email protected], Lei
Xie1,2, [email protected].
2:20 - 61 - Cheminformatics career at the
Royal Society of Chemistry, UK
Colin Batchelor, [email protected],
17 - Encoded Library Technology data
analysis: Finding the grain of sand you want
without getting a sunburn
Kenneth E Lind, [email protected], Neil
R Carlson, Ninad V Prabhu, Jeff A Messer.
2:50 - 62 - Patent law as a non-traditional
career in chemistry
Sarah P Hasford,
[email protected],
3:20 - Intermission
19 - How to highlight hits: Advances in visual
data analytics tools for HTS data
Jesse A. Gordon,
[email protected], Jess Sager.
3:35 - 63 - Role of personal interests,
motivation, and timing in the transitioning to
a new career
Svetla Baykoucheva, [email protected],
26 - iBIOMES: Managing and sharing large
biomolecular simulation datasets in a
distributed environment with iRODS
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3.
4:05 - 64 - From the bench to the board
Rebecca Boudreaux,
[email protected],
4:35 - 65 - Political "science": Opportunities
for chemists in science policy
Ticora V Jones, [email protected],
28 - New cheminformatics microscopes:
Combining semantic web technologies,
cheminformatical representations, and
chemometrics for understanding and
predicting chemical and biological properties
Egon L Willighagen,
[email protected],
5:05 - Concluding Remarks
Monday, April 8, 2013
31
Chemical Information Bulletin Vol. 65(1) Spring 2013
29 - Discovery of TLR2 antagonists by virtual
screening
Manuela S Murgueitio1, [email protected], Sandra Santos-Sierra2, Gerhard
Wolber1.
66 - From virtual screening to real taste
modulators: Bitter blockers and sweetness
enhancers
Quoc Tuan Do2,
[email protected], Terry L.
Peppard1, John Scire1, Philippe Bernard2.
31 - On the compound annotation and
cleaning the GSK screening collection
initiative: The utility of an Inhibition
Frequency Index (IFI)
Subhas J Chakravorty,
[email protected], James A
Chan, Juan Luengo, Nicole M Greenwood,
Ioana Popa-Burke, Ricardo Macarron.
67 - Navigation through chemogenomics
data with SPID
Austin B Yongye1, José L Medina-Franco2,
[email protected].
68 - Inferring odor detection threshold (ODT)
using chemical structure based properties
Jae Hong Shin, [email protected],
Sebastian E. Ahnert, David J. Wild, Yong-Yeol
Ahn.
32 - Analyzing screening and similarity
searching outcome in light of multiple
approaches to the same target
Tina Garyantes, [email protected],
70 - ChEMBL tools and services: Creating
bridges between cheminformatics and
bioinformatics
Mark Davies, [email protected], Louisa J.
Bellis, A. Patricia Bento, Jon Chambers, Anna
Gaulton, Anne Hersey, Yvonne Light, George
Papadatos, John P. Overington.
33 WITHDRAWN
36 - From hits to leads: Data visualization of
chemical scaffolds beyond traditional SAR
exploration
Tyler Peryea, [email protected], John
Braisted, Ajit Jadhav, Rajarshi Guha, Noel
Southall, Dac-Trung Nguyen.
72 - About the impact of open access
bioassay data on cheminformatic
approaches
Barbara Zdrazil,
[email protected], Gerhard F.
Ecker.
41 - Reproducible research applied to
cheminformatics experiments
Paul J Kowalczyk,
[email protected],
80 - PubChem BioAssay: A public database
for chemical biology data
Yanli Wang, [email protected],
46 - Reverse pharmacognosy: From
molecules to active ingredients
Quoc Tuan Do,
[email protected], Sylvain
Blondeau, Philippe Bernard.
84 - Open PHACTS: Meaningful linking of
preclinical drug discovery knowledge
Egon L Willighagen1,
[email protected],
Christian Brenninkmeijer2, Chris T Evelo1, Lee
Harland3, Alasdair J.G. Gray2, Carole Goble2,
Andra Waagmeester1, Antony J Williams4.
59 - From studying block copolymers to
chemical information: A journey of an
alternative chemistry career as an academic
science librarian
Vincent F Scalfani, [email protected],
32
Chemical Information Bulletin Vol. 65(1) Spring 2013
89 - Making hidden data discoverable: How
to build effective drug discovery engines?
Sebastian Radestock,
[email protected], Jürgen SwientyBusch.
118 - Mining frequent itemsets: Constructing
topological pharmacophores using
pharmacophore feature pairs
Paul J Kowalczyk,
[email protected],
92 - Chemical science that underpins the
Reaxys database
Juergen Swienty-Busch1, [email protected], Pieder Caduff2, David
Evans2.
119 - Lexichem: Not another chemical
nomenclature app
Edward O Cannon,
[email protected],
Tuesday, April 9, 2013
96 - Intuitive and integrated browsing of
reactions, structures, and citations: The
Roche experience
Fausto Agnetti1, Michael Bensch1, Hermann
Biller1, Martin Blapp1, Ben Cheikh2, Gerd
Blanke1, Joerg Degen1, Bernard Dienon1,
Thomas Doerner1, Gunther Doernen1, Frieda
Farshchian1, Werner Gotzeina1, Peter Hilty1,
Ralf Horstmoeller1, Thomas Jeker1, Brian
Jones1, Michael Kappler2,
[email protected], Aslam Momin2,
Antonio Regoli1, Denis Ribaud1, Bernard
Starck1, Daniel Stoffler1, Klaus Weymann1,
Padmanabha Udupa2.
Linking Bioinformatic Data and
Cheminformatic Data - AM Session
Morial Convention Center
Room: 349
Ian Bruno, John Overington, Organizers
Ian Bruno, Presiding
8:15 am - 11:55 am
8:15 - Introductory Remarks
8:20 - 69 - Integrating chemical and
biological structural information
Gary Battle, [email protected], Jose Dana,
Saqib Mir, Tom Oldfield, Sameer Velankar,
Gerard Kleywegt.
101 - ALOHA-MPS: A novel compound
scoring and selection tool
Rishi R Gupta1, [email protected],
Steven W Muchmore1, Derek A Debe2, Philip J
Hajduk1.
8:45 - 70 - ChEMBL tools and services:
Creating bridges between cheminformatics
and bioinformatics
Mark Davies, [email protected], Louisa J.
Bellis, A. Patricia Bento, Jon Chambers, Anna
Gaulton, Anne Hersey, Yvonne Light, George
Papadatos, John P. Overington.
109 - Novel in silico prediction algorithms for
the design of stable and more effective
proteins
Francisco G Hernandez-Guzman,
[email protected], Velin
Spassov, Lisa Yan.
9:10 - 71 - Pharmacological profiling of drugs
by linking chemoinformatics and
bioinformatics data
Olivier Taboureau, [email protected],
110 - Advanced structural modeling of
biologics with BioLuminate
David A Pearlman, Tyler Day, Kathryn Loving,
David Rinaldo, Noeris Salam, Dora
Warshaviak, Kai Zhu, Woody Sherman,
[email protected].
9:35 - 72 - About the impact of open access
bioassay data on cheminformatic
approaches
33
Chemical Information Bulletin Vol. 65(1) Spring 2013
Barbara Zdrazil,
[email protected], Gerhard F.
Ecker.
8:35 - 77 - PubChem: A community driven
resource
Evan Bolton, [email protected],
10:00 - Intermission
9:05 - 78 - NCI/CADD chemical structure Web
services
Markus Sitzmann, [email protected],
Alexey V. Zakharov, Laura Guasch Pàmies,
Marc C. Nicklaus.
10:15 - 73 - Biological target identification
through combination of 3D molecular
similarity and lexical similarity of clinical
effects
Emmanuel R Yera, [email protected], Ann E
Cleves, Ajay N Jain, [email protected].
9:35 - 79 - ChemSpider: Disseminating data
and enabling an abundance of chemistry
platforms
Antony J Williams1, [email protected], Valery
Tkachenko1, Ken Karapetyan1, Alexey
Pshenichnov1, Dmitry Ivanov1, Colin
Batchelor2, Jon Steele2, David Sharpe2.
10:40 - 74 - In silico prediction of gene
expression profiles for drug-like compounds
based on their structural formulae
Alexey Lagunin, [email protected],
Sergey Ivanov, Anastassia Rudik, Dmitry
Filimonov, Vladimir Poroikov.
10:05 - Intermission
10:20 - 80 - PubChem BioAssay: A public
database for chemical biology data
Yanli Wang, [email protected],
11:05 - 75 - CAS’ bioactivity and target
indicators provide new insights for scientists
working at the interface of chemistry and
biology
Roger Schenck, [email protected],
10:50 - 81 - Chemistry-related resources at
the Protein Data Bank in Europe
Gary Battle, [email protected], Gerard
Kleywegt, Sameer Velankar, Tom Oldfield,
Swanand Gore, Saqib Mir, Jose Dana.
11:30 - 76 - Jikitou biomedical question
answering system: Using multiple resources
to answer biomedical questions
Michael A. Bauer1,2, [email protected],
Robert E. Belford3, Daniel Berleant1, Roger A.
Hall1.
11:20 - 82 - Architecture for an open science
molecular compound database
Egon L Willighagen,
[email protected],
Tuesday, April 9, 2013
11:50 - Concluding Remarks
Public Databases Serving the Chemistry
Community - AM Session
Morial Convention Center
Room: 350
Tuesday, April 9, 2013
Linking Bioinformatic Data and
Cheminformatic Data - PM Session
Morial Convention Center
Room: 349
Antony Williams, Sean Ekins, Organizers
Sean Ekins, Presiding
8:30 am - 11:55 am
8:30 - Introductory Remarks
34
Chemical Information Bulletin Vol. 65(1) Spring 2013
engines?
Sebastian Radestock,
[email protected], Jürgen SwientyBusch.
Ian Bruno, John Overington, Organizers
John Overington, Presiding
1:55 pm - 5:30 pm
1:55 - 83 - Linking chemical biology
information within PubChem
Evan Bolton, [email protected],
5:05 - 90 - Applying the law of parsimony in
molecular design
Alberto Del Rio, [email protected],
2:20 - 84 - Open PHACTS: Meaningful linking
of preclinical drug discovery knowledge
Egon L Willighagen1,
[email protected],
Christian Brenninkmeijer2, Chris T Evelo1, Lee
Harland3, Alasdair J.G. Gray2, Carole Goble2,
Andra Waagmeester1, Antony J Williams4.
Tuesday, April 9, 2013
Public Databases Serving the Chemistry
Community - PM Session
Morial Convention Center
Room: 350
2:45 - 85 - Extracting more value from data
silos: Using the semantic web to link
chemistry and biology for innovation
Derek Scuffell1, [email protected],
Philip Ashworth2.
Antony Williams, Sean Ekins, Organizers
Antony Williams, Presiding
2:00 pm - 5:25 pm
3:10 - 86 - Roundtripping between smallmolecule and biopolymer representations
Noel M O'Boyle1,
[email protected], Evan Bolton2,
Roger A Sayle1.
2:05 - 91 - Local and remote tracking of
molecular dynamics data for global
dissemination
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3.
3:35 - Intermission
2:35 - 92 - Chemical science that underpins
the Reaxys database
Juergen Swienty-Busch1, [email protected], Pieder Caduff2, David
Evans2.
2:00 - Introductory Remarks
3:50 - 87 - Representing and registeristing
antibody-drug conjugates
Keith T Taylor, [email protected],
Burton L Leland, William L Chen, Young-Mi
Kwon.
3:05 - 93 - ChemReact: A free database
containing more than 524,000 reactions
available at your fingertips
Valentina Eigner-Pitto, [email protected],
Hans Kraut, Heinz Saller, Heinz Matuszczyk,
Josef Eiblmaier, Peter Loew.
4:15 - 88 - Mining chemical and biological
data for trends: Visualizing structured
numeric data from ELNs
Philip J Skinner,
[email protected], Phil McHale,
Amy Kallmerton, Megean Schoenberg, Anis
Khimani, Kate Blanchard, Michael Swartz.
3:35 - Intermission
3:50 - 94 - Navigating between patents,
papers, abstracts, and databases using public
sources and tools
4:40 - 89 - Making hidden data discoverable:
How to build effective drug discovery
35
Chemical Information Bulletin Vol. 65(1) Spring 2013
Christopher Southan1, Sean Ekins2,
[email protected].
[email protected], Travis T
Wager, Xinjun J Hou, Patrick R Verhoest.
4:20 - 95 - ChemSpider reactions: Delivering
a free community resource of chemical
syntheses
Valery Tkachenko1, [email protected],
Colin Batchelor2, Ken Karapetyan1, David
Sharpe2, Antony J Williams1.
9:05 - 98 - Multi-criteria drug discovery:
Recent results in building predictive models,
combining predictions, and generating new
chemistry ideas
Brian B Masek, [email protected],
Fabian Boes, Richard Cramer, Roman
Dorfman, Stephan Nagy, Lei Wang, Bernd
Wendt.
4:50 - 96 - Intuitive and integrated browsing
of reactions, structures, and citations: The
Roche experience
Fausto Agnetti1, Michael Bensch1, Hermann
Biller1, Martin Blapp1, Ben Cheikh2, Gerd
Blanke1, Joerg Degen1, Bernard Dienon1,
Thomas Doerner1, Gunther Doernen1, Frieda
Farshchian1, Werner Gotzeina1, Peter Hilty1,
Ralf Horstmoeller1, Thomas Jeker1, Brian
Jones1, Michael Kappler2,
[email protected], Aslam Momin2,
Antonio Regoli1, Denis Ribaud1, Bernard
Starck1, Daniel Stoffler1, Klaus Weymann1,
Padmanabha Udupa2.
9:35 - 99 - Implementation of multi-criteria
decision making (MCDM) tools in early drug
discovery processes
Marie Ledecq, [email protected],
10:05 - Intermission
10:20 - 100 - Being suitably sensitive:
Balancing competing performance criteria
for in silico models
Robert D Clark, [email protected],
Marvin Waldman, Jinhua Zhang, Adam C. Lee,
Michael S. Lawless.
5:20 - Concluding Remarks
10:50 - 101 - ALOHA-MPS: A novel compound
scoring and selection tool
Rishi R Gupta1, [email protected],
Steven W Muchmore1, Derek A Debe2, Philip J
Hajduk1.
Wednesday, April 10, 2013
Balancing Chemistry on the Head of a Pin:
Multi-Parameter Optimization - AM Session
Morial Convention Center
Room: 349
11:20 - 102 - Finding multi-parameter rules
for successful optimization
Matthew Segall, [email protected],
Iskander Yusof, Edmund Champness.
Edmund Champness, Matthew Segall,
Organizers
Edmund Champness, Matthew Segall,
Presiding
8:30 am - 11:50 am
Wednesday, April 10, 2013
Public Databases Serving the Chemistry
Community - AM Session
Morial Convention Center
Room: 350
8:30 - Introductory Remarks
8:35 - 97 - Exploiting a more polar property
space in the design of brain penetrant
molecules
Anabella Villalobos,
36
Chemical Information Bulletin Vol. 65(1) Spring 2013
8:30 - Introductory Remarks
Computational De novo Protein and Peptide
Design - PM Session
Morial Convention Center
Room: 349
Cosponsored by COMP
8:35 - 103 - Universal SMILES: Finally, a
canonical SMILES string?
Noel M O'Boyle, [email protected],
Rachelle Bienstock, Organizers
Rachelle Bienstock, Presiding
1:30 pm - 3:10 pm
9:05 - 104 - Analysis of tautomerism in
databases of commercially available
compounds
Laura Guasch, [email protected], Markus
Sitzmann, Marc C Nicklaus.
1:30 - Introductory Remarks
Antony Williams, Sean Ekins, Organizers
Antony Williams, Sean Ekins, Presiding
8:30 am - 11:55 am
1:45 - 109 - Novel in silico prediction
algorithms for the design of stable and more
effective proteins
Francisco G Hernandez-Guzman,
[email protected], Velin
Spassov, Lisa Yan.
9:35 - 105 - RSC chemical validation and
standardization platform: A potential path to
quality-conscious databases
Ken Karapetyan1, [email protected],
Valery Tkachenko1, Colin Batchelor2, David
Sharpe2, Antony Williams1.
2:10 - 110 - Advanced structural modeling of
biologics with BioLuminate
David A Pearlman, Tyler Day, Kathryn Loving,
David Rinaldo, Noeris Salam, Dora
Warshaviak, Kai Zhu, Woody Sherman,
[email protected].
10:05 - Intermission
10:20 - 106 - Challenges and
recommendations for obtaining chemical
structures of industry-provided repurposing
candidates
Christopher Southan1, Anthony J Williams2,
Sean Ekins3, [email protected].
2:35 - 111 - Virtual mutagenesis for
optimizing antibody binding affinity: A
prospective study
Enrico O. Purisima, [email protected],
Vivcharuk Victor, Traian Sulea, Denis L'Abbé,
Yves Durocher, Jason Baardsnes, Maureen
O'Connor.
10:50 - 107 - One size fits all or how to find
the needle in the haystack?
Juergen Swienty-Busch, [email protected],
3:00 - Concluding Remarks
Wednesday, April 10, 2013
11:20 - 108 - Pistoia Alliance AppStore: Apps
for life sciences R&D
Alex M Clark, [email protected],
Advances in Virtual High-Throughput
Screening - PM Session
Morial Convention Center
Room: 350
11:50 - Concluding Remarks
Wednesday, April 10, 2013
Joel Freundlich, Sean Ekins, Organizers
Sean Ekins, Presiding
1:30 pm - 4:50 pm
37
Chemical Information Bulletin Vol. 65(1) Spring 2013
4:20 - 118 - Mining frequent itemsets:
Constructing topological pharmacophores
using pharmacophore feature pairs
Paul J Kowalczyk,
[email protected],
1:30 - Introductory Remarks
1:35 - 112 - Setting up a discovery pipeline in
KNIME and PipelinePilot: High-throughput
de novo design utilizing gigantic virtual
chemistry spaces
Carsten Detering, [email protected],
4:45 - Concluding Remarks
2:00 - 113 - New targets addressed by
DEKOIS 2.0: Demanding evaluation kits for
objective in-silico screening
Frank M. Boeckler, [email protected], Matthias R Bauer, Tamer M. I.
M. Abdelrehim, Simon M. Vogel.
Thursday, April 11, 2013
General Papers - AM Session
Morial Convention Center
Room: 349
Jeremy Garritano, Organizers
Jeremy Garritano, Presiding
8:00 am - 10:45 am
2:25 - 114 - PubChem3D: A virtual screening
platform
Evan Bolton, [email protected],
8:00 - Introductory Remarks
2:50 - Intermission
8:05 - 119 - Lexichem: Not another chemical
nomenclature app
Edward O Cannon,
[email protected],
3:05 - 115 - Dual-event machine learning
models to accelerate drug discovery
Sean Ekins1,2, [email protected], Robert
C Reynolds3,4, Hiyun Kim5, Mi-Sun Koo5,
Marilyn Ekonomidis5, Meliza Talaue5, Steve
Paget5, Lisa Woolhiser6, Anne J Lenaerts6,
Barry A Bunin1, Nancy Connell5, Joel S
Freundlich5,7.
8:30 - 120 - Teach our naming tool to be
bilingual: Chinese name-to-structure
conversion
David Deng, [email protected], Daniel
Bonniot.
3:30 - 116 - Virtual high-throughput
screening of novel pharmacological agents
based on PASS predictions
Vladimir V. Poroikov1,2,
[email protected], Dmitry A.
Filimonov1, Alexey A. Lagunin1, Tatyana A.
Gloriozova1, Olga A. Tarasova1, Pavel V.
Pogodin1,2, Marc C. Nicklaus3.
8:55 - 121 - Community based curation of
chemical images extracted using automated
routines
Valery Tkachenko1, [email protected],
Dmitry Ivanov1, Colin Batchelor2, Antony J
Williams1.
9:20 - Intermission
3:55 - 117 - How GPUs can find your next hit:
Accelerating virtual screening with OpenCL
Simon Krige1, [email protected],
Mark Mackey1, Simon McIntosh-Smith2,
Richard Sessions2.
9:30 - 122 - Investigation of tautomerization
and its impact on the content and data
model for RSC ChemSpider
Ken Karapetyan1, [email protected],
Valery Tkachenko1, Colin Batchelor2, David
Sharpe2, Antony J Williams1.
38
Chemical Information Bulletin Vol. 65(1) Spring 2013
10:20 - 124 - Algorithm for efficient
conformational equivalence testing without
a priori atomic correspondence or
connectivity information
Gregory R. Magoon1,2,
[email protected], William H. Green2.
9:55 - 123 - Structure-activity relationships of
combinatorial data sets: Rapid identification
of selectivity switches in positional scanning
libraries tested across formyl peptide
receptors
José L Medina-Franco1, [email protected],
Clemencia Pinilla2, Jon R Appel2, Marc A
Giulianotti1, Radleigh Santos1, Bruce S
Edwards3, Larry A Sklar3, Richard A
Houghten1.
Cosponsored Symposia
Emilio Esposito, Scott Wildman Monday,
April 8, 2013
10:15 - 72 - Computational investigation of
the mechanisms for small molecule
antagonists of pRb inactivation by HPV-E7
Ara Abramyan, Zhiwei Liu, Vojislava
Pophristic.
Chairs' Prime Choices - AM Session Six More
Cool Talks #6coolTalks
Morial Convention Center
Room: 357
Cosponsored by BIOL, CINF, MEDI, PHYS,
PROF, YCC
10:45 - 73 - Developing polarizable potentials
for metal-organic materials sorption
simulations
Christian R Cioce, Keith McLaughlin, Brant
Tudor, Ashley Mullen, Jonathan L Belof, Brian
Space.
Emilio Esposito, Organizers
Emilio Esposito, Presiding
8:30 am - 11:45 am
11:15 - 74 - Exploring residue component
contributions to dynamical network models
of allostery
Adam T. VanWart, John Eargle, Zaida LutheySchulten, Rommie E. Amaro.
8:30 - 69 - Role of water bridged hydrogen
bonds in ubiquinone binding geometries at
the Qi site of cytochrome bc1
Bao-Linh Nguyen, Ralph A Wheeler.
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
9:00 - 70 - Cluster-enhanced lipid partitioning
in membrane domains
Zhenlong Li, Alemayehu A Gorfe.
Collaborative Drug Discovery for Neglected
Diseases - PM Session
Morial Convention Center
Room: 357
Cosponsored by BIOL, CINF, COMP, MEDI,
PHYS, PROF, TOXI, YCC
9:30 - 71 - Molecular dynamics simulations of
uranyl-peroxide nanocapsules in aqueous
solution
Bess Vlaisavljevich, Pere Miró, Shuxian Hu,
Allison Dzubak, Riccardo Spezia, Christopher J.
Cramer, Laura Gagliardi.
Johanna Jansen, Rommie Amaro, Wendy
Cornell, Y. Jane Tseng, Organizers
10:00 - Intermission
39
Chemical Information Bulletin Vol. 65(1) Spring 2013
Rommie Amaro, Presiding
1:30 pm - 5:35 pm
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
1:30 - 397 - Judging the ACS Teach-DiscoverTreat initiative: Lessons learned and
directions for the future
W. Patrick Walters
Emilio Esposito, Organizers
Seonah Kim, Presiding
8:30 am - 11:45 am
8:30 - 7 - Autocatalytic and cooperativelystabilized dissociative adsorption of water on
stepped metal surfaces
Davide Donadio, Rengin Pekoz, Svenja
Worner, Luca M Ghiringhelli, Luigi Delle Site.
2:05 - 398 - Structural plasticity of malarial
dihydroorotate dehydrogenases
demonstrated by X-ray structural analysis of
inhibitor bound complexes
Xiaoyi Deng, Farah El Mazouni, Elizabeth J.
Goldsmith, Pradipsinh K. Rathod, Margaret A.
Phillips.
9:00 - 8 - Role of environment in the catalysis
of the MutY DNA repair enzyme
Elizabeth Brunk, Jeremey S Arey, Ursula
Rothlisberger.
2:40 - 399 - TDT 2012 Grand Champion: 3DQSAR-boosted SBVS
Paolo Tosco
9:30 - 9 - 6N-D water and small molecule
distributions from 3D-RISM
Daniel J. Sindhikara, Fumio Hirata.
3:15 - Intermission
3:30 - 400 - Cresset Award: Teaching
molecular interactions with online interactive
pharmacophore modeling
David R Koes, Carlos J Camacho.
10:00 - Intermission
10:15 - 10 - Predicting the displacement of
water molecules from protein hydration sites
due to small molecule binding
David J Huggins
4:05 - 401 - KNIME Award: Computational
workflow for human African trypanosomiasis
phosphodiesterase inhibitor identification
Khaled M Elokely, Robert J Doerksen.
10:45 - 11 - Advances in the treatment of
water in drug discovery: Applications to
affinity and selectivity design
Robert Abel, Goran Krilov, Lingle Wang,
Woody Sherman.
4:40 - 402 - OpenEye Award: Public domain
chemical databases for neglected disease
drug discovery
George Nicola, Tiqing Liu, Michael Gilson.
5:15 - Panel Discussion
11:15 - 12 - Long-range hydrogen-bond
structure in aqueous solutions
Richard H Henchman, Sheeba J Irudayam.
COMP, Emilio Esposito, Scott Wildman
Sunday, April 7, 2013
COMP, Emilio Esposito, Scott Wildman
Sunday, April 7, 2013
Computational Study of Water - AM Session
#H2O is like OxyClean(R). It Catalyzes in
Biological Systems and Materials!
Morial Convention Center
Computational Study of Water - PM Session
#H2O @interfaces == Water at Interfaces.
Morial Convention Center
40
Chemical Information Bulletin Vol. 65(1) Spring 2013
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizers
Robert Paton, Presiding
1:30 pm - 5:15 pm
1:30 - 35 - WITHDRAWN
Emilio Esposito, Organizers
Sami Jaffar, Presiding
8:30 am - 11:45 am
2:00 - 36 - Effects of charge transfer on ion
adsorption to the liquid water/vapor interface
Marielle Soniat, Steven W. Rick.
8:30 - 75 - Liquid water from first principles:
The importance of exact exchange, dispersion
interactions, and nuclear quantum effects
Robert A. DiStasio Jr., Biswajit Santra,
Zhaofeng Li, Roberto Car.
2:30 - 37 - Computational studies of aqueous
and ionic liquids interfaces
liem dang
9:00 am 76 WITHDRAWN
3:00 - Intermission
9:30 - 77 - Development of a polarizable
water model for solution simulations
Hao Hu
3:15 - 38 - Crossing the line: Thermodynamic
and structural signatures of methane
hydration across the water-vapor interface
Jesse Spencer, Riccardo Baron, Valeria
Molinero.
10:00 - Intermission
3:45 - 39 - Probing vapor-liquid nucleation of
water with advanced simulation method
Troy D Loeffler, Bin Chen.
10:15 - 78 - How different is ionic and
hydrophobic solvation: DFT vs. point charge
models
Marcel D Baer, Christopher J Mundy, Gregory
K Schenter.
4:15 - 40 - Modeling vibrational sumfrequency spectra of dicarboxylic acids at the
water/air interface
Nicholas A Valley, Geraldine L Richmond.
10:45 - 79 - Approaches for getting
benchmark structures and thermodynamics
of large water clusters
Berhane Temelso, George C. Shields.
4:45 - 41 - Water under nanoscopic
hydrophobic confinement: Phase behavior,
sublimation mechanism, and a novel
monolayer ice
Andrew L Ferguson, Nicolas Giovambattista,
Peter J Rossky, Athanassios Z
Panagiotopoulos, Pablo G Debenedetti.
11:15 - 80 - Properties of water and ice from
DFT simulations
Joost VandeVondele
COMP, Emilio Esposito, Scott Wildman
Sunday, April 7, 2013
Drug Discovery - AM Session Target-Based:
Having the Target in Site for #DrugDisco is
More Than Half the Battle #GIjoe
Morial Convention Center
Room: 353
Cosponsored by CINF, MEDI
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
Computational Study of Water - AM Session
Developing a Deeper Understanding of #H2O
41
Chemical Information Bulletin Vol. 65(1) Spring 2013
Drug Discovery - PM Session Ligand-Based:
We Got your Ligands for Ya! #DrugDisco
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Zoe Cournia, Presiding
8:30 am - 11:45 am
8:30 - 13 - Design of novel TLR antagonists by
molecular modeling
Manuela S Murgueitio, Sandra Santos-Sierra,
Gerhard Wolber.
Scott Wildman, Y. Jane Tseng, Organizers
Caley Allen, Presiding
1:30 pm - 5:15 pm
9:00 - 14 - Discovery of novel Arp2/3
inhibitors through computer-aided design
George Patargias, Andrew W Baggett, Bradley
J Nolen, Zoe Cournia.
1:30 - 42 - Whole template CoMFA applies
benefits of topomer alignments within the
original CoMFA context
Richard D Cramer
9:30 - 15 - Computer-aided Design in Drug
Discovery: Featuring case studies of
pharmacological targets in prostate cancer
Eleonora Gianti, Randy J Zauhar.
2:00 - 43 - Design of new potent inhibitors for
the GSK3-beta kinase
N. R. Jena
10:00 - Intermission
2:30 - 44 - Application of fragment-based
drug design to the discovery of novel anti-HIV
microbicides
Olga Tarasova, Dmitry Filimonov, Vladimir
Poroikov.
10:15 - 16 - Computational approaches in
designing allosteric inhibitors for ITK kinase
Ray J Unwalla, David R Anderson, David C
Limburg, Charlie Choi, Mihir D Parikh, Ravi
Kurumbail, Ann Aulabaugh, Weidong Ding,
Nicole Caspers, Seungil Han, Jeffrey Ohren,
Hong Wang, Quintus Medley, Subarna
Shakya.
3:00 - 45 - Pharmacophore models of
competitive TRPV1 antagonists based on
open data
Daria A. Tsareva, Gerhard F. Ecker.
10:45 - 17 - Structural recognition between
TWEAK and Fn14: A prelude to discovery of
inhibitors for Fn14-TWEAK association
Pooja Narang, Harshil Dhruv, Joseph Loftus,
Joachim Petit, Michael Berens, Nhan Tran,
Nathalie Meurice.
3:30 - Intermission
3:45 - 46 - Scaffold hopping for aromatic
rings: Can MM compete with QM?
Tim Cheeseright, Mark Mackey.
4:15 - 47 - Conformational and
pharmacophoric features within the
macrocyclic spiroimine toxins family
Rómulo Aráoz, Jordi Molgó, Bogdan I. Iorga.
11:15 - 18 - Hydration entropy from computer
simulations
Roland G Huber, Julian E Fuchs, Susanne von
Grafenstein, Monika Laner, Hannes G.
Wallnöfer, Nemja Abdelkader, Romano T
Kroemer, Klaus R Liedl.
4:45 - 48 - Predictive models to better
understand the nuances for the oximereactivation of cyclosarin, sarin, tabun, and
VX inactivated acetylcholinesterase
COMP, Emilio Esposito, Scott Wildman
Sunday, April 7, 2013
42
Chemical Information Bulletin Vol. 65(1) Spring 2013
Emilio Xavier Esposito, Terry R Stouch, Troy
Wymore, Jeffry D Madura.
11:15 - 86 - QSAR modeling of imbalanced
high-throughput screening data in PubChem
Alexey V Zakharov, Markus Sitzmann, Marc C
Nicklaus.
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
Drug Discovery - AM Session Methodology:
Old Problems Require New Solutions.
#DrugDisco #answersToYourProblems
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Drug Discovery - PM Session Chemical and
Structural Informatics: The Most Valuable
Commodity I Know of is Information. Gordon Gekko #informatics #WallStreet
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Kameron Jorgensen, Presiding
8:30 am - 11:45 am
Scott Wildman, Y. Jane Tseng, Organizers
Terry Stouch, Presiding
1:30 pm - 5:15 pm
8:30 - 81 - Automated planning of relative
free energy calculations
David L Mobley, Shuai Liu, Teng Lin, Yujie Wu,
Robert Abel.
1:30 - 110 - Measuring complexity and selfsimilarity of chemical structures in drug
discovery
Modest von Korff, Thomas Sander.
9:00 - 82 - Binding site models for affinity
prediction guided by protein structure
Rocco Varela, Ajay N Jain.
2:00 - 111 - Knowledge-based chemical
fragment analysis in protein binding sites
Edith Chan, David Selwood, Roman Laskowski.
9:30 - 83 - Enhanced sampling in ligand and
polypeptide docking with Glide
Matt Repasky, Jay Banks, Annabhimoju
Ramakrishna, Ivan Tubert-Brohman.
2:30 - 112 - Return of the tautomers: Toward
a global model of tautomerism
Robert Fraczkiewicz, Marvin Waldman,
Robert D. Clark, Walter S. Woltosz.
10:00 - Intermission
10:15 - 84 - Integration of cheminformatics
and molecular simulations approaches for
accurate prediction of native-like ligand
binding poses
Regina Politi, Feng Ding, Nikolay V Dokholyan,
Alexander Tropsha.
3:00 pm 113 WITHDRAWN
3:30 - Intermission
3:45 - 114 - Protein mapping using FTMap
with user-defined probe sets
Scott E Mottarella, Dima Kozakov, Sandor
Vajda.
10:45 - 85 - ProBiS tools: Algorithm, database,
and web-server for predicting and modeling
of pharmaceutically interesting proteins
Dusanka Janezic
4:15 - 115 - Statistical limits of molecular
scoring
43
Chemical Information Bulletin Vol. 65(1) Spring 2013
Gregory A Ross, Garrett M Morris, Philip C
Biggin.
Thorsten Köddermann, Axel W Arnold, Dirk
Reith.
4:45 - 116 - Boosting virtual screening
enrichments using data fusion: Coalescing 2D
fingerprints, shape, and docking
G. Madhavi Sastry, Woody Sherman.
10:45 - 155 - Chemistry-Wide Association
Studies (CWAS): Determining joint mutagenic
effects of co-occurring chemical features
Yen Low, Alexander Sedykh, Denis Fourches,
Alexander Golbraikh, Alexander Tropsha.
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
11:15 - 156 - Progress in predicting pKa of
drug-like molecules with ab initio methods
Art D. Bochevarov, Dale A. Braden, Dean M.
Philipp, Jeremy R. Greenwood.
Drug Discovery - AM Session ADME/Tox:
Designing the Drug is Easy. The Hard Part is
Understanding How the Drug Interacts
#DrugDisco @acsCOMPprog
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI, TOXI
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
Drug Discovery - PM Session Chemical and
Structural Informatics: Information is Power
#DrugDisco #informatics
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI, TOXI
Scott Wildman, Y. Jane Tseng, Organizers
Kira Armacost, Kira Armacost, Presiding
8:30 am - 11:45 am
8:30 - 151 - Bioclipse-OpenTox: Interactive
predictive toxicology
Egon Willighagen, Barry Hardy, Nina
Jeliazkova, Ola Spjuth.
Scott Wildman, Y. Jane Tseng, Organizers
Eleonora Gianti, Presiding
1:30 pm - 5:15 pm
9:00 - 152 - Development of QSAR models for
prediction of hepatotoxicity using postmarket data from FDA's AERS database
Xiao Zhu, Barbara L. Minnier, Naomi L.
Kruhlak.
1:30 - 183 - Enhancing high throughput
screening for Mycobacterium tuberculosis
drug discovery using Bayesian models
Sean Ekins, Robert C Reynolds, Baojie Wan,
Scott G Franzblau, Joel S Freundlich, Barry A
Bunin.
9:30 - 153 - Consensus prediction of skin
permeability and sensitization using
cheminformatics approaches
Eugene Muratov, Vinicius Alves, Denis
Fourches, Judy Strickland, Carolina Andrade,
Alexander Tropsha.
2:00 - 184 - Exact solution to the DNA and
protein alignment problem
Milan Randic
10:00 - Intermission
2:30 - 185 - Use and abuse of structural data
in model validation and analysis
John W Liebeschuetz, Oliver S Smart.
10:15 - 154 - Accurate calculations of
partition coefficients (log POW and log PMW)
with atomistic simulation methods
3:00 - 186 - Strategic design of non-covalent
interactions in small molecule drug discovery
Rajiah Aldrin Denny
44
Chemical Information Bulletin Vol. 65(1) Spring 2013
3:30 - Intermission
Michael L Mayo, David Hogle, Svetlana V
Kilina.
3:45 - 187 - Data are not sufficient: Making
the difference in cross-functional project
team decisions is the objective
David A. Evans, Juergen Swienty-Busch,
Pieder Caduff.
3:00 - Intermission
3:15 pm 52 WITHDRAWN
3:45 - 53 - ššQuantitative structural solution
of rare earth doped disordered up-conversion
material β-NaLaF4
Tara M Michels-Clark, Michal Chodkiewicz,
Robert J Harrison, Christina Hoffmann, Jürg
Hauser, Anthony Linden, Vickie Lynch,
Thomas Weber, Hans-Beat Bürgi.
4:15 - 188 - False false positives - problem or
red herring?
Mark D Mackey, Timothy J Cheeseright.
4:45 - 189 - Ups and downs of conformer
generation: Challenges and solutions derived
from structural data
Robin Taylor, Jason C Cole, Oliver Korb,
Patrick McCabe.
4:15 - 54 - Effect of capping ligands on optical
properties of PbSe quantum dots
Mary Margaret Hedrick, Svetlana V Kilina.
COMP, Emilio Esposito, Scott Wildman
Sunday, April 7, 2013
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
Material Science - PM Session These
Materials Rock! #matSci
Morial Convention Center
Room: 354
Cosponsored by CINF, COLL, PHYS, PMSE,
POLY
Material Science - PM Session More Material
Madness #matSci
Morial Convention Center
Room: 356
Cosponsored by CINF, COLL, PHYS, PMSE,
POLY
Maciej Haranczyk, Organizers
Luke Achenie, Presiding
1:30 pm - 4:45 pm
Maciej Haranczyk, Organizers
Cheng-Tsung Lai, Presiding
1:30 pm - 5:20 pm
1:30 - 49 - Efficient and precise techniques for
parallel kinetic Monte Carlo simulations
Jerome P Nilmeier
1:30 - Introductory Remarks
1:35 - 117 - Surface modified TiO2
photocatalysts: Insights from first principles
simulations
Anna Iwaszuk, Michael Nolan.
2:00 - 50 - Investigation of methods for the
simulation of cross-linked epoxy networks
and property prediction using molecular
dynamics
Vanessa Oklejas, Jason de Joannis.
2:05 - 118 - Surface reactivity/stability and
hydration of calcium silicate phases
Can Ataca, Engin Durgun, Hamlin H. Jennings,
Jeffrey C. Grossman.
2:30 - 51 - Computational study of the
stability and diameter dependence of polycarbazole wrapped single-walled carbon
nanotubes
45
Chemical Information Bulletin Vol. 65(1) Spring 2013
2:35 - 119 - Computational investigation of
reactions at metal/water interfaces
Muhammad Faheem, Andreas Heyden.
2:00 - 191 - Molecular dynamics study of the
Cytolysin A pore forming toxin using atomistic
and coarse grained simulations
Swarna M Patra, Rajat Desikan, Prabal K
Maiti, Ganapathy Ayappa.
3:05 - 120 - Building a chemical intuition
under pressure: Prediction of polyhydride and
subhydride phases
Eva Zurek
2:30 - 192 - Ras dynamics, membrane binding,
and assembly
Alemayehu A Gorfe, Zhenlong Li, Hualin Li.
3:35 - Intermission
3:00 - 193 - Molecular dynamics and
enhanced sampling simulations of a
membrane-bound reaction center protein
David N LeBard
3:50 - 121 - Computational study on the
proton affinity and thermophysical properties
of imidazole derivatives
Haining Liu, Jason E Bara, C. Heath Turner.
3:30 - Intermission
4:20 - 122 - Computational screening of mixed
metal halide ammines
Peter Bjerre Jensen, Steen Lysgaard, Ulrich
Quaade, Tejs Vegge.
3:45 - 194 - Probing the Meta I to Meta II
equilibrium of rhodopsin activation in
detergent micelles with molecular dynamics
simulations
Blake Mertz, Michael F Brown, Edward
Lyman.
4:50 - 123 - Crystallization of ionic lipid
membranes, elucidated by atomistic
simulation
Baofu Qiao, Monica Olvera de la Cruz.
4:15 - 195 - What can we learn from
microsecond simulations of a peripheral
membrane protein of yeast?
Brent Rogaski, Jeffery B. Klauda.
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
Membranes - PM Session Inner Leaflet
#InsaneInTheMembrane #throwback
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, COLL, PHYS
4:45 - 196 - Fatty acid amide hydrolase
(FAAH) substrate specificity understood via
molecular dynamics
Giulia Palermo, Pablo Campomanes, Marilisa
Neri, Daniele Piomelli, Andrea Cavalli, Ursula
Rothlisberger, Marco De Vivo.
Michael Feig, Organizers
Amber Carr, Presiding
1:30 pm - 5:15 pm
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
Membranes - PM Session Outer Leaflet
#membraneInsanity #outerSpace
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, COLL, PHYS
1:30 - 190 - Probing the deprotonation
mechanism of the His37 tetrad in the M2
channel from the influenza A virus via
molecular simulation
Hao Dong, Michael L Klein, Giacomo Fiorin.
46
Chemical Information Bulletin Vol. 65(1) Spring 2013
Michael Feig, Organizers
Adam VanWart, Presiding
1:30 pm - 4:45 pm
Room: 357
Cosponsored by CINF, MEDI
Scott Wildman, Organizers
Scott Wildman, Presiding
8:30 am - 11:45 am
1:30 - 418 - Coarse-grained molecular
dynamics of PEGylated assemblies
Sharon M. Loverde, Wataru Shinoda, Dennis
E. Discher, Michael L. Klein.
8:30 - 367 - TB Mobile: Appifying data on
antituberculosis molecule targets
Sean Ekins, Alex M Clark, Malabika Sarker,
Carolyn Talcott, Barry A Bunin.
2:00 - 419 - Nanoparticle-membrane
interactions: Insights from coarse-grained MD
simulations
Paraskevi Gkeka, Panagiotis Angelikopoulos,
Zoe Cournia.
9:00 - 368 - Mobile + Cloud: A replacement
for desktop cheminformatics?
Alex M Clark
2:30 - 420 - Oxygen diffusion in water,
alkanes, and lipid bilayers
An Ghysels, Richard M Venable, Richard W
Pastor, Gerhard Hummer.
9:30 - 369 - Molecular modeling on iOS
devices
Warren Hehre
3:00 - Intermission
10:00 - Intermission
3:15 - 421 - Lipid 12: Accurate membrane
simulations with a redesigned modular
phospholipid force field for AMBER
Ross C Walker, Benjamin Madej, Ian R Gould,
Callum J Dickson.
10:15 - 370 - Expanding the reach of
cheminformatics through mobile computing
Steven M Muskal
10:45 - 371 - iMolview: A multiplatform
mobile application for biologists and chemists
Maxim Totrov, Eugene Raush, Ruben
Abagyan.
3:45 - 422 - Dissecting lipid–protein
interaction in ABC transporters
Ronald D. Hills, Jr
11:15 - 372 - Facilitating collaborative
molecular visualization using mobile PyMOL
Jason Vertrees
4:15 - 423 - Exploring ion channel activity with
multi-microsecond molecular dynamics
simulations
Igor Vorobyov, Céline Boiteux, Scott E. Feller,
Toby W. Allen.
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
Nanosimulations and Nanoinformatics - PM
Session Big Talks About Little Things
#nanoInfo #nanoSims
Morial Convention Center
Room: 351
Cosponsored by BIOL, CINF, MEDI, TOXI
Mobile Applications - AM Session Can you
Calculate Me Now? (Tweet Along with Us!
Use #compMobile)
Morial Convention Center
47
Chemical Information Bulletin Vol. 65(1) Spring 2013
Alexander Tropsha, Organizers
Alexander Tropsha, Presiding
1:30 pm - 5:25 pm
5:20 - Concluding Remarks
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
1:30 - Introductory Remarks
Poster Session - EVE Session
Morial Convention Center
Room: Hall A, Sec D
Cosponsored by ANYL, CHED, CINF, COLL,
MEDI, ORGN, PHYS, PMSE, POLY
1:35 - 431 - Inorganic nanographenes:
Innovations by computations
Zhongfang Chen
2:05 - 432 - Computational nanotoxicology:
Nano-QSARs, protein-ligand docking, and
quantum-chemical methods for toxicity
prediction of nanoparticles
Bakhtiyor Rasulev, Danuta Leszczynska, Jerzy
Leszczynski.
Emilio Esposito, Organizers
6:00 pm - 8:00 pm
219 - Chemical bonding in graphene, its
derivatives, and several polycyclic aromatic
hydrocarbons
Alexander I Boldyrev, Ivan A Popov.
2:35 - 433 - Impact of biological endpoints on
the descriptor pool: Using decorated
nanotubes to understand the role of spatial
descriptors
Chi-Yu Shao, Sing-Zuo Chen, Bo-Han Su,
Yufeng J Tseng, Emilio Xavier Esposito, Anton
J Hopfinger.
220 - Hydration free energy calculations show
that amino acid hydrophobicity is strongly
environment-dependent
Kimberly S Keyes, Pavel V Klimovich, David L
Mobley.
3:05 - 434 - Exploring mechanistic inference
of decorated nanotubes using multiple
descriptor classes
Yufeng J Tseng, Chi-Yu Shao, Sing-Zuo Chen,
Bo-Han Su, Emilio Xavier Esposito, Anton J
Hopfinger.
221 - MP2 and DFT study of the selectivity of
NADP binding sites for novel ligands
Rachel K Sanders, Mauricio Cafiero.
222 - MP2 and DFT calculations of
interactions of boronated and non-boronated
intercalants in small nucleic acid models
Ashley Tufton, Mauricio Cafiero.
3:35 - Intermission
3:50 - 435 - Adsortion and oxidation of
ethanol on Pt-particles supported by
defective graphene
Yixuan Wang, Zhenfeng Xu.
223 - Application of alchemical binding free
energy calculations and other computational
methods to aid the discovery of antibacterial
drugs
Vivian Jaber
4:20 - 436 - From metal to molecules: Probing
the limits of melting in small gallium clusters
Nicola Gaston, Krista G. Steenbergen.
224 - MP2 and DFT analysis of the ligand
selectivity of two sulfotransferase enzymes
Diana Bigler, Hallie Weems, Mauricio Cafiero.
4:50 - 437 - Simulating “soft” electronics
Timothy Clark
225 - Acceleration of quantum chemistry and
chemical similarity calculations on GPGPU
48
Chemical Information Bulletin Vol. 65(1) Spring 2013
architecture toward faster virtual screening
Ryota Koga, Yuki Furukawa, Koji Yasuda,
Naoki Nariai.
234 - Computational studies of the molecular
mechanisms responsible for Ca2+ permeation
and Mg2+ block of NMDA receptors
Lea Veras, Igor Kurnikov, Jon W Johnson,
Maria Kurnikova.
226 - Binding energies of electron-rich and
electron-deficient stacked arene-arene
complexes: Substituent effects and SAPT
analysis
Laura K Hardebeck, Michelle Watt, Charles C
Kirkpatrick, Michael Lewis.
235 - Application of fast Fourier transforms
on frequency-modulated continuous-wave
radars
Dwayne M Brooks, Jamiiru Luttam
Luttamaguzi, Akbar Eslami.
227 - Computer simulations of crystallization
of the ionic liquid [dmim+][Cl-] in the bulk
Xiaoxia He, Francisco R Hung, Erik E Santiso.
236 - Exploration of mechanism between
nanotoxicity and protein targets: QSAR
models using nanotoxicity endpoints of
decorated nanotubes
Chi-Yu Shao, Sin-Zuo Chen, Bo-Han Su.
228 - CrystalDock: Leveraging known
structural information for fragment-based
drug design
Aaron J Friedman, Jacob D Durrant, James A
McCammon.
237 - New approach of traditional Chinese
medicine taxonomy: Using marker ingredients
as bases
Kuo-Hsiang Hsu, Yufeng J. Tseng.
229 - Ab initio electronic structure program
Jaguar: New in version 8.0
Art D. Bochevarov
238 - Development of OPLS-AA force field
parameters for ionic liquid simulations and
their applications in elimination reactions
Somisetti V Sambasivarao, Caley Allen,
Orlando Acevedo.
230 - Molecular dynamics simulation of the
interaction between cholates and cholesterol
Madeline Reed
231 - How molecular interactions between
terpenoid mosquito repellents and
attractants may affect repellency?
Shengliang Liao, Zongde Wang, Jie Song,
Guorong Fan, Shangxin Chen, Peng Wang,
Jinzhu Chen.
239 - Multi-ligand docking in the minor
groove of DNA
Chrystal D Bruce, Maddi Ferrara.
240 - Molecular modeling of the ionic liquid
[EMIM+][TFMSI-] confined in model
nanoporous materials
Nav N Rajput, Joshua Monk, Ramesh Singh,
Francisco R Hung.
232 - Estimating activation free energy for
hydration of perfluoroaldehyde and glyoxal
Osamu Setokuchi
241 - Targeting the alternative gene splicing
related proteins: Identification of potent and
selective cdc2-like (Clk) kinase inhibitors
Min Shen, Andrew S. Rosenthal, Bryan T.
Mott, Cordelle Tanega, Douglas S. Auld,
Christopher P. Austin, David J. Maloney, Craig
J. Thomas.
233 - Q-Chem 4.1: The latest advances in
methods and algorithms in the Q-Chem
program package
Zhengting Gan, Evgeny Epifanovskiy, Emil
Proynov, Yihan Shao.
49
Chemical Information Bulletin Vol. 65(1) Spring 2013
242 - C-H activation of cycloalkanes with the
Cp'Rh(CO) fragment: A computational study
Amanda L Renz, Michael B. Hall.
250 - Computational approach to the
prediction of enzyme specificities
David B Williams-Young, Jaeju Ko, Mary Jo
Ondrechen.
243 - Structural modeling of the relaxin
peptide receptor and its small molecule
agonists
Xin Hu, Zaohua Huang, Noel Southall, Jingbo
Xiao, Catherine Z. Chen, Elena Barnaeva, Juan
J. Marugan, Marc Ferrer, Wei Zheng, Irina U.
Agoulnik, Alexander I. Agoulnik.
251 - BindingDB: A protein-ligand database
for drug discovery
George Nicola, Tiqing Liu, Linda Hwang,
Michael Gilson.
252 - Classification tree and random forest
based prediction models on molecular
autofluorescence
Yi-Shu Tu, Tze-Hao Lin, Yufeng J Tseng.
244 - Elucidation of the molecular
interactions between neuraminidase and
sialic acid
Alvin R Wu, Leah Krause, Adam Van
Wynsberghe.
253 - Heat of formation of ethenone
Kevin Range, Julia Tiaw.
254 - Quantum mechanical studies of
thiohydroxycarbene
Jean M. Standard
245 - Computational investigation of the
interactions of lysyl oxidase with its natural
substrates
Michael Lynch, Daniel Turman, Faina Ryvkin.
255 - Investigating substrate-induced
conformational changes in alkanesulfonate
monooxygenase using molecular dynamics
simulations
Kira A Armacost, Symon Gathiaka, Holly Ellis,
Orlando Acevedo.
246 - Investigation of the effects of electronic
desolvation on oseltamivir binding kinetics to
N1 influenza neuraminidase
Carmen M Montagnon, Robert B Clayton,
Adam W. Van Wynsberghe.
247 - Exploring ionic liquid induced
mechanistic changes for β-elimination
reactions from QM/MM simulations
Caley R Allen, Somisetti V Sambasivarao,
Orlando Acevedo.
256 - Computing relative acidities of phenol
derivatives in DMSO and water with
isodesmic equations
Katherine L. Munroe, David H. Magers.
257 - Relative acidities of barbituric acid and
thiobarbituric acid
Jonathan E. Landrum, Katherine L. Munroe,
David H. Magers.
248 - QM/MM simulations for the elucidation
of ionic liquid effects upon classical organic
reactions
Caley R Allen, Orlando Acevedo.
258 - Computational studies of isomers of C80
Taylor McKee, J. Paige Buchanan, David H.
Magers.
249 - Energetic and structural basis for DNA
damage recognition by human 8-oxoguanine
glycosylase
Haoquan Li, Dmitry O Zharkov, Carlos de Los
Santos, Arthur P Grollman, Carlos Simmerling.
259 - Relative stabilities of derivatives of 6methylpentacene and 6-methylene-6,13-
50
Chemical Information Bulletin Vol. 65(1) Spring 2013
dihydropentacene
Marika Zarafyan, Bei Cao, David H. Magers.
268 - Estimating protein-protein electrostatic
binding energetics: A feature-based approach
Amelia B Kreienkamp, Mala L Radhakrishnan,
Finale Doshi-Velez.
260 - Characterization of excited states via
FFT time-correlation functions: IR spectrum
for conjugated molecules
Johan F Galindo Cruz, Sebastian FernandezAlberti, Adrian E Roitberg.
269 - Comparison of resonance-assisted
hydrogen bonding in carboxyphosphate and
structural analogs
Sebastien Hebert, Venkata Pakkala, Steven
Firestine, Jeffrey Evanseck.
261 - Calculating enthalpies of formation for
the oxadiazoles and their cyano derivatives
via isodesmic and homodesmotic reactions
Shelby L. Raines, Sarah E. DeLee, Erica Q.
Chong, Glake Hill, David H. Magers.
270 - Molecular dynamics simulations of
bacterial interaction with hydrophilic surfaces
Divesh Bhatt
262 - Determining the protonation state of
the active site residues of Laminaripentaoseproducing β-1,3-glucanase
Shuhua Ma, Xiaochen Zhang.
271 - Effects of ethanol on the toll-like
receptor 3 - RNA complex: A molecular
dynamics study
Chinthaka N Ratnaweera, Steven R Gwaltney.
263 - Conventional strain energies of the
diazetidines and the diphosphetanes
Shelley A. Smith, Ashley R. McDonald, Patricia
H. Stewart, Glake Hill, David H. Magers.
272 - Development and implementation of
multilevel Generalized Distributed Data
Interface in GAMESS
Alexander Gaenko, Ryan Olson, Mark S
Gordon.
264 - Computational insight to molecular
imprinting
Julia M Saloni
273 - LMRSDCI method in GAMESS:
Localization, parallelization, and performance
analysis
Alexander Gaenko, David Krisiloff, Mark S
Gordon, Emily A Carter.
265 - Computational analysis of the
electrostatic interaction between chronic
myeloid leukemia drugs and Bcr-Abl kinase
Lucy Y Liu, Mala L Radhakrishnan.
274 - Influenza fusion peptides prime lipids
for membrane fusion using specific
interactions
Sébastien Légaré, Patrick Lagüe.
266 - Extension of Redfield theory: Inclusion
of non-elastic collisions
Shin-ichiro Sato
275 - Assessment of correction methods for
intramolecular basis set superposition error
xavier barbeau, Patrick Lagüe.
267 - Virtual screening for new γaminobutyric acid transporter 1 inhibitors
based on insights acquired by comparative
modeling
Andreas Jurik, Barbara Zdrazil, Harald H Sitte,
Gerhard F Ecker.
276 - Analysis of chemical networks: A novel
paradigm for optimal synthesis
Chris M Gothard, Nosheen A Gothard, Bartosz
A Grzybowski.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
277 - Effects of lipid binding on the structure
of human paraoxanase1
Steven Gwaltney, Manikanthan Bhavaraju.
285 - Elucidating the mechanism of action of
unnatural amino acid containing antimicrobial
peptides in membrane environments
Tiffany D Clark, Libero Bartolotti, Rickey P.
Hicks.
278 - C-O bond cleavage using transition
metal catalysts: From dimethyl ether
activation to lignin degradation
Cong Liu, Angela K Wilson.
286 - Antibacterial drug leads targetting
isoprenoid biosynthesis: Toward inhibitors of
undecaprenyl pyrophosphate synthase
William Sinko, Wei Zhu, Yonghui Zhang,
Steffen Lindert, Cesar AF de Oliveira, Eric
Oldfield, J. Andrew McCammon.
279 - Calculation of redox potentials of type-I
blue copper proteins using quantum
mechanical/molecular mechanical simulations
Thomas G. Bartholow, Sudeep Bhattacharyya,
Sudeep Bhattacharyya.
287 - Quantum chemical studies on the
mechanism and selectivity of indole direct
arylations
Sami K Jaffar, Simone Tomasi, Robert S Paton.
280 - Versatility of chloroperoxidase catalytic
function: Apoenzyme tunes reactivity of the
active center
Alexander N. Morozov, Armando D. Pardillo,
David C. Chatfield.
288 - Halogen bonding in rational drug design:
Targeting histidine
Andreas Lange, Markus O Zimmermann,
Rainer Wilcken, Frank M Boeckler.
281 - Disulfide bond in human neuroglobin
determines heme-apoenzyme hydrogen
bonding: A possible mechanism for redox
control of neuroprotective activity
David C. Chatfield, Alexander N. Morozov,
James P. Roach.
289 - Organocatalysts for biorenewable
desymmetrization
Milan Cvitkovic, David Alberg, Gretchen
Hofmeister, Daniela Kohen.
282 - Simultaneous loop prediction for
homology modeling
Steven V Jerome, Richard A Friesner.
290 - Insights into the long-time dynamics,
structural properties, and thermalstabilities of
serine hydrolase enzymes from molecular
dynamics and normal mode analysis
Habib U Rehman, Steven R Gwaltney.
283 - Quantum chemical studies of the
binding and catalytic hydride transfer reaction
of flavin with aromatic substrates
Caitlin Bresnahan, Yer Yang, Sudeep
Bhattacharyya.
291 - Theoretical study of the electronic
structure of gold clusters over graphene
Alan Miralrio, Luis E Sansores.
284 - Information-driven fully flexible
HADDOCKing: Performance on a benchmark
of protein-ligand complexes
Jeffrey S Grinstead, Tracy L Wormwood,
Aurelien Thureau, Rolf Boelens, Alexandre
M.J.J. Bonvin.
292 - Rational modulation of enzymeinhibitor residence time for the
mycobacterium tuberculosisenoyl-ACP
reductase InhA
Cheng-Tsung Lai, Pan Pan, Nina Liu, Weixuan
Yu, Lauren Spagnuolo, Sonam Shah, Gopal R.
Bommineni, Peter Tonge, Carlos Simmerling.
52
Chemical Information Bulletin Vol. 65(1) Spring 2013
293 - Conformational and structural dynamics
of K-ras and H-ras proteins: Specificity at the
catalytic domain?
Nandini Rambahal, Harrison H. Hocker,
Alemayehu A. Gorfe.
302 - Bringing clarity to the prediction of
protein-ligand binding free energies via
blurring
Melek N. Ucisik, Zheng Zheng, John C. Faver,
Kenneth M. Merz Jr..
294 - Modeling of potent and selective kappa
opioid receptor peptide inhibitors in light of
the X-ray crystal structure
Karina Martinez-Mayorga, Kendal G. Byler,
Austin B. Yongye, Marc A. Giulianotti, Colette
T. Dooley, Richard A. Houghten.
303 - Molecular dynamics investigation of
CD44 hyaluronan binding domain with sialic
acid-terminal N-glycans
Christina E. Faller, Olgun Guvench.
304 - Exploring the conformational landscape
of decaprenyl pyrophosphate synthase, a
promising drug target against tuberculosis
Meekyum O Kim, William Sinko, César de
Oliveira, Eric Oldfield, J. Andrew McCammon.
295 - Molecular modeling of trypanosomal
cathepsins
Karina Martinez-Mayorga, Kendall G. Byler.
296 - Polarizable force field OPLS-AAP applied
to proteins and carbon surfaces
Patric Schyman, William L. Jorgensen.
305 - Oxygen diffusion pathways in a
cofactor-independent oxygenase
Natali V Di Russo, Heather L Condurso, Steven
D Bruner, Adrian E Roitberg.
297 - Novel approach to detect and visualize
aggregation-prone residues in
immunoglobulins
Elizabeth Sourial
306 - Linear relationship between computed
energies and pKa for carboxylic acids and
amides
Obsa L Bokku, Melissa C Denler, Joseph D Alia.
298 - Rationalization and visualization of nonbonded interactions using extended Hückel
theory
Alain Ajamian
307 - Natural bond orbitals related to the pKa
of carboxyl acids and phenols
Abdala Bashir, Tiwaloluwa Ajibewa, Finhas
Ogbazghi, Joseph D Alia.
299 - Computational docking of pyrazole
derivatives into CYP2E1
Joseph W. Levy, Grover P. Miller, Martin D.
Perry, Jr..
308 - Structural models for the interaction of
pentamidine analogs with the NMDA receptor
Madhusoodanan Mottamal, Michael L Berger,
Jean Jacques Vanden Eynde, Dorota
Maciejewska, Ivana Jarak, Tien L Huang.
300 - Theoretical investigation of the
reactivity of Ir(II) sulfides, Ir2(μ-S)2(PPh3)4 and
Ir2(μ-S)2(PH3)4
Stella Kritikou, Michael B. Hall.
309 - Aggregation-volume-bias Monte Carlo
investigation of vapor-liquid nucleation at
varying dimensionalities: A comparison to
classical nucleation theory
Andrew Galtas, Troy D Loeffler, Bin Chen.
301 - Organic solvent-induced conformational
transition of an amphiphilic peptide
Quentin R. Johnson, Ricky Nellas, Tongye
Shen.
310 - Comparison of coarse-grained and
atomistic-level simulations for aminoacyl
53
Chemical Information Bulletin Vol. 65(1) Spring 2013
tRNA-synthetases
Alexander M Strom, Sudeep Bhattacharyya,
Sanchita Hati.
318 - Theoretical modeling of silicon halides
David G Hogle, Svetlana V Kilina.
319 - Graphene oxide together with carbon
nanotubes: A computational study
Daniel B Lawson
311 - Automated docking receptor selection
workflow for non-nucleoside reverse
transcriptase drug discovery
Richard A Stanton, Kyle A Brown, Karan
Uppal, Kim M Gernert, James H Nettles,
Raymond F Schinazi.
320 - Iron (ii) complex spin crossover
characteristics
Heather Leask, Pascal Lacroix, Pascal Lacroix,
Jose-Antonio Real.
312 - On reproducing the intrinsic reaction
path by specific reaction parameters in
semiempirical methods
Shuai Liang, Adrian E Roitberg.
321 - Molecular dynamics of the Hsp70
chaperone's Nucleotide Binding Domain:
Understanding nucleotide binding and
structure-function relationships
Ewa I Golas, Cezary Czaplewski, Adam Liwo,
Harold A Scheraga.
313 - Force field development for thiolated
gold nanoclusters
Maegan N Dailey, Sandipan Banerjee, Jose A
Gascon.
322 - Calculated pKa values for amino acid
side chains near the ubiquinone and
ubiquinol binding sites of cytochrome bc1
Ralph A Wheeler, Bao-Linh Nguyen.
314 - Leveraging structural knowledge gained
from accelerated molecular dynamics
simulations of IspG and IspH to inform
development of novel inhibitors of the nonmevalonate pathway
Patrick G Blachly, César de Oliveira, J. Andrew
McCammon.
323 - Unraveling the twist: Designing Mobius
twist molecules
Christopher V Donnay, Sharaai Marrero,
Camilla Montonen, Michelle M Francl.
315 - Conformation-dependent aggregation
of lipid-anchored Ras and its effect on
membrane curvature
Hualin Li, Alemayehu Gorfe.
324 - Simulation studies of ether-alkane
mixtures adsorbed on solid substrates
James Lee, Selena R. Watkins, Kelly E.
Anderson, J. Ilja Siepmann.
316 - Towards the identification of small
molecule Ras inhibitors: A dynamics-guided
approach
Harrison Hocker, Nandini Rambahal,
Alemayehu Gorfe.
325 - Electronic effects of
Zn(II)tetrakis(phenyl)porphyrin encapsulation
into a Zn(II) carboxylate MOF, USF1
Christi L Whittington, Randy W Larsen, H Lee
Woodcock.
317 - Comparing post Hartree-Fock models
with DFT for the gas-phase dissociation of
branched aminonitile moieties
William D Price, Hannah E Bott, Charles
Doerner, Kristina Gemayel.
326 - Theoretical comparison of C-H
activation rates of CpRh(R); R=CO or CNCH3
Joana E Cisneros, Amanda Renz, Michael Hall.
327 - Validation of a tuned interfacial
parameter set using dual-force-field
54
Chemical Information Bulletin Vol. 65(1) Spring 2013
CHARMM for the accurate simulation of
protein adsorption on a silica glass surface
James Snyder, Tigran Abramyan, Jeremy A
Yancey, Steven J Stuart, Robert A Latour.
Sally R Ellingson, Jeremy C Smith, Jerome
Baudry.
328 - Do androids dream of electronic
documents?
Ron Massicotte
336 - Structural assessment for active and
selective kinase inhibitors: GSK-3β and CDK2
case studies
Khaled M Elokely, Gang Fu, Robert J
Doerksen.
329 - Improved nucleic acid descriptors for
siRNA efficacy prediction
Simone Sciabola, Robert Stanton, Qing Cao,
Ignacio Faustino, Modesto Orozco.
337 - Dynamical network models of allostery
for hisH-hisF without alpha-carbons
Adam T. VanWart, John Eargle, Zaida LutheySchulten, Rommie E. Amaro.
330 - DNA damage induced by electrophilic
alkylating agents generated from
nitrosoureas: A theoretical investigation of
mechanism and structure-carcinogenicity
relationship
Lijiao Zhao, Rugang Zhong, Tingting Liu.
338 - Characterization of the wide-open flap
state of Klebsiella aerogenes urease
Benjamin Roberts, Bill Miller III, Adrian
Roitberg, Kenneth Merz, Jr.
331 - Ras conformational dynamics: Novelreaction coordinates and role of conserved
waters
Priyanka Prakash, Abdallah Sayyed-Ahmad,
Alemayehu A Gorfe.
340 - Vibronic switching of fluorescence
output from urea-functionalized poly (pphenylene) receptor by fluoride-anion
recognition
Yanai Kazuma, Shimada Ryotaro, Fuchise
Keita, Kakuchi Ryohei, Sakai Ryosuke, Satoh
Toshifumi, Kakuchi Toyoji, Sato Shin-ichiro.
339 WITHDRAWN
332 - Potential surface editing to accelerate
conformational searching
Joseph T Allison, Anthony K Rappé.
341 WITHDRAWN
342 - Novel method for computer-based
entropy estimation: Application to model
molecular processes
James Robertson, Victor Holanda Rusu,
Riccardo Baron.
333 - Fast and accurate prediction of drug
binding affinity by similarity-based docking
and machine learning
Michal Brylinski
334 - Solid state adaptive natural density
partitioning: A tool for deciphering chemical
bonding in periodic systems
Timur R. Galeev, Benjamin D. Dunnington, J.
R. Schmidt, Alexander I. Boldyrev.
343 - Characterizing and exploiting the
properties of water in protein active sites for
rational drug design and discovery
Tom Kurtzman Young
344 - Novel coarse-grained force field for
carbohydrates
Victor H Rusu, Riccardo Baron, Roberto D Lins.
335 - Acceleration of high-throughput
molecular docking for novel drug discovery on
supercomputers
55
Chemical Information Bulletin Vol. 65(1) Spring 2013
345 - Cross-docking to identify antibodyantigen interaction partners
Krishna Praneeth Kilambi, Jeffrey J Gray.
354 - Ensemble molecular dynamics approach
to characterizing the protein-ligand complex:
Residual inhibitor entropy enhances drug
potency
Amethyst Radcliffe, Benjamin Pham,
Samantha Cao, Phuc La, Eric Sorin, Richard
Wang, Yi An.
346 - Structurally aligned local sites of activity
(SALSAs) computational method for the
prediction of function of structural genomics
proteins
Joslynn S Lee, Mary Jo Ondrechen.
355 - Diagrammatic vibrational structure
methods for molecules and solids
Matthew R Hermes, Murat Keçeli, So Hirata.
347 - Time-dependent density functional
theory-based modeling of functionalization of
cyclohexasilane and related compounds
David G Hogle, Svetlana V Kilina.
356 - Application of the free energy
perturbation method to monoamine
transporters
Kalyan Immadisetty, Jeffry D Madura.
348 WITHDRAWN
349 - Assessing the applicability of pairwise
alternatives to Ewald summation on a wide
range of ionic liquids
Billy Wayne McCann, Orlando Acevedo.
357 - Quantitative structure-activity
relationships (QSAR) for oral chemical health
guidance values
Yunfeng Tie, G. Sarah Sirin, James S. Holler,
Eugene Demchuk.
350 - Modular amber lipid force field for the
simulation of complex membranes and
membrane bound proteins
Benjamin D Madej, Callum J. Dickson, Ross C
Walker, Ian R. Gould.
358 - So many models... which one should I
choose?
Adam C Lee, Robert Fraczkiewicz, Walter S
Woltosz.
351 - Off-Path simulation method: A new
chain-of-replica approach for sampling
reaction processes
Justin K White, Milan Hodoscek, Henry L
Woodcock.
359 - Crystallographic waters: To displace or
not to displace?
Alexander S. Bayden, Demetri T. Moustakas,
Diane Joseph-McCarthy, Michelle L. Lamb.
360 - RNA/peptide binding driven by
electrostatics: Insights from bi-directional
pulling simulations
Trang N Do, Paolo Carloni, Gabriele Varani,
Giovanni Bussi.
352 - Computational study of the selective
dispersing of single-walled carbon nanotubes
by ssDNA
Chantel I. Nicolas
353 - Solvent effects and dynamic averaging
of 195Pt NMR shielding in cisplatin derivatives
using ab inito molecular dynamics (MD) and
DFT
Kiplangat Sutter, Jochen Autschbach, Lionel
Truflandier.
361 WITHDRAWN
362 - Global optimization techniques utilized
to generate new accurate VLE force fields for
ethylene oxide as a test case
Andreas Krämer, Marco Hülsmann, Jadran
Vrabec, Dirk Reith.
56
Chemical Information Bulletin Vol. 65(1) Spring 2013
363 - Using compendia as a collaborative tool
in neglected diseases drug discovery
Paul J Kowalczyk
10:00 - 89 - Polarizable atomic multipolebased AMOEBA force field for proteins
Pengyu Ren
364 - Free energetics of polyarginine peptides
in model lipid bilayers via molecular dynamics
simulations
Sandeep Patel, Yuan Hu.
10:30 - Intermission
10:45 - 90 - Developing force fields to run on
specialized hardware
John L Klepeis, David E Shaw.
365 - Molecular dynamics study of spanning
networks of protein hydration water
Sandeep Patel, Di Cui.
11:15 - 91 - Force-field development for
computer simulation of biomolecular
systems: The GROMOS case
Wilfred F. van Gunsteren
366 - Structure of 1-Benzyl-1H-tetrazol-5amine studied by X-ray diffraction, DFT
calculations, NMR, FTIR and UV-visible
spectra
Ayyaz Mahmood, Ricardo Luiz Longo.
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
Potential Function Uncertainty and
Validation - AM Session Predictions and
Benchmarking
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
Potential Function Uncertainty and
Validation - AM Session Potential Model
Development
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 am - 11:45 am
9:00 - 157 - Next generation of benchmarks
for non-covalent interactions, and challenges
from charge penetration effects
C. David Sherrill
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 am - 11:45 am
9:00 - 87 - Toward a comprehensive
polarizable macromolecular force field based
on the CHARMM classical drude oscillator
model
Alexander D. MacKerell Jr.
9:30 - 158 - Development of new density
functionals and their validation against broad
databases
Roberto Peverati, Donald G. Truhlar.
9:30 - 88 - Accurate and efficient quantum
chemical methods for structures and noncovalent interactions in large bio- and supramolecular systems
Stefan Grimme
10:00 - 159 - Prediction of structure and
binding affinity of protein-protein complexes
Alexandre M.J.J. Bonvin
10:30 - Intermission
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Potential Function Uncertainty and
Validation - AM Session Uncertainty
Estimation
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
10:45 - 160 - Prediction of binding affinities
with a Poisson-Boltzmann continuum solvent
model
Junmei Wang
11:15 - 161 - Can we predict what is
predictable? UsingMarkov State Models to
elucidate robustness of potentials in
molecular simulation
Vijay S. Pande
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
8:30 am - 11:15 am
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
8:30 - 450 - Fragment-based methods for
error estimation in biomolecular modeling
John C. Faver, Kenneth M. Merz.
Potential Function Uncertainty and
Validation - AM Session Predictions and
Benchmarking
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
9:00 - 451 - Placing rigorous bounds on
uncertainty in quantum chemical energy and
structural optimisation calculations
Alistair P Rendell, Pete Janes.
9:30 - 452 - Equilibrium simulations of protein
folding as a force field test
Stefano Piana, Kresten Lindorff-Larsen, David
E Shaw.
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 am - 11:00 am
9:00 - 386 - Next generation of databases for
benchmark binding energies
Kevin E. Riley
10:00 - Intermission
10:15 - 453 - Sensitivity and uncertainty
analysis for dispersion-corrected density
functional theory
Felix Hanke
9:30 - 387 - Binding assays by computer
simulations: Capabilities, accuracy, and
precision
Gianni D De Fabritiis
10:45 - 454 - Bayesian calibration of potential
energy surfaces
Christopher S Simmons
10:00 - 388 - Computing binding affinities of
supramolecular host-guest systems
Hari S. Muddana, Michael K. Gilson.
COMP, Emilio Esposito, Scott Wildman
Monday, April 8, 2013
10:30 - 389 - Virtual docking and affinity
prediction: Insights from benchmarking and
validation studies
Enrico O. Purisima, Traian Sulea, Hervé
Hogues.
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - PM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
COMP, Emilio Esposito, Scott Wildman
Thursday, April 11, 2013
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Rama Kondru, Sung-Sau So, Vickie Tsui,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
Presiding
1:30 pm - 4:45 pm
Presiding
8:30 am - 12:15 pm
8:30 - 144 - MD and lead optimization: An
evolving relationship
Christopher Bayly
1:30 - 104 - Alchemical calculations of binding
free energies from MD simulations
David L Mobley, Gabriel J Rocklin.
9:00 - 145 - Mechanism to trigger unfolding in
alkylguanine alkyltransferase
Elizabeth Brunk, Birgit Mollwitz, Ursula
Rothlisberger.
2:00 - 105 - Novel approaches to study
protein-ligand interactions
Kenneth M Merz
9:30 - 146 - Structural and mechanistic
insights on Ca2+–independent phospholipase
A2 enzymes through MD simulations and
isotope-exchange experiments
Denis Bucher, Varnavas D Mouchils, Edward A
Dennis, J Andrew McCammon.
2:30 - 106 - Efficient optimization of enzyme
inhibitors via free energy calculations
William L. Jorgensen
3:00 - Intermission
10:00 - 147 - Affixing the acylation gap:
Elucidating DD-peptidase catalyzed betalactam reaction mechanisms
Jacqueline C. Hargis, Justin K. White, H. Lee
Woodcock.
3:15 - 107 - Recognition of Gleevec by Srcfamily kinases
Benoit Roux, Yen-Lin Lin.
3:45 - 108 - Computation of relative binding
free energy for an inhibitor and its analogs
binding with Erk kinase using thermodynamic
integration MD simulation
Kuan-Wei Wu, Po-Chin Chen, Jun Wang, YingChieh Sun.
10:30 - Intermission
10:45 - 148 - Halogen bonding: From
quantum chemistry to molecular design and
chemical biology
Frank M. Boeckler, Rainer Wilcken, Markus O.
Zimmermann, Andreas Lange, Andreas C.
Joerger.
4:15 pm 109 WITHDRAWN
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
11:15 - 149 - Heme-based nitric oxide release:
Predicting reaction mechanisms via
computational structure activity relationship
studies
Sai Lakshmana Vankayala, Jacqueline C
Hargis, Henry L Woodcock.
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - AM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
11:45 - 150 - PDB ligand conformational
energies calculated quantum-mechanically
Markus Sitzmann, Iwona E Weidlich, Igor V
Filippov, Chenzhong Liao, Megan L Peach,
Wolf-Dietrich Ihlenfeldt, Rajeshri G Karki,
Rama Kondru, Sung-Sau So, Vickie Tsui,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Yulia V Borodina, Raul E Cachau, Marc C
Nicklaus.
docking
Dahlia A Goldfeld, Richard A Friesner.
COMP, Emilio Esposito, Scott Wildman
Tuesday, April 9, 2013
4:15 - 180 - Virtual screening against
comparative protein structure models
Hao Fan, Andrej Sali, Brian K. Shoichet.
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - PM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
4:45 - 181 - Wscore: An empirical scoring
function for protein-ligand binding which
incorporates the water structure of the active
site
Richard A. Friesner
Vickie Tsui, Sung-Sau So, Rama Kondru,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
Presiding
1:30 pm - 5:45 pm
5:15 - 182 - Unique electronic environment
and contact direction sensitive scoring
function for predicting affinities of proteinligand complexes in Contour®
Suresh B Singh
1:30 - 175 - Accurate ligand docking and
screening: Lessons from the Pocketome
Ruben Abagyan, Yu-chen Chen, Andrey
Ilatovskiy, Irina Kufareva, Fiona McRobb,
Manuel Rueda, Maxim Totrov.
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - AM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
2:00 - 176 - Algorithms for discovering small
molecules that stabilize specific protein
conformations
Ryan G. Coleman, Marcus Fischer, Khanh Vuu,
Brian K. Shoichet, James S. Fraser.
Rama Kondru, Sung-Sau So, Vickie Tsui,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
Presiding
8:30 am - 11:45 am
2:30 - 177 - Novel methods to determine and
exploit protein flexibility for ligand discovery
Marcus Fischer, Ryan G. Coleman, James S.
Fraser, Brian K. Shoichet.
8:30 - 373 - Consistent modeling of
protein/nucleic acid small molecule
interactions from free energies to ionization
equilibrium
Charles L. Brooks III
3:00 - 178 - Flexible CDOCKER: Combining
grid-based docking with pseudo-explicit
structure based methods in CHARMM
Jessica K Gagnon, Charles L Brooks III.
3:30 - Intermission
9:00 - 374 - Target-ligand interactions: Next
generation modeling
Jose Duca, Robert Pearlstein, Daniel McKay.
3:45 - 179 - Can't wait for crystallography?
Novel methods for GPCR loop prediction and
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Chemical Information Bulletin Vol. 65(1) Spring 2013
9:30 - 375 - Extending MixMD to allosteric
systems
Phani Ghanakota, Heather A Carlson.
Dahlia R Weiss, SeungKirl Ahn, Maria F
Sassano, Andrew C Kruse, Joel Karpiak, Bryan
L Roth, Brian K Kobilka, Brian K Shoichet,
Robert J Lefkowitz.
10:00 - Intermission
2:30 - 405 - Toward the accurate and efficient
identification of novel human soluble epoxide
hydrolase inhibitors via in-silico methods
Camilo Velez-Vega, Crystal Nguyen, Michael
K. Gilson, Sung-Hee Hwang, Kin Sing Stephen
Lee, Bruce D. Hammock.
10:15 - 376 - Protein flexibility and ligand
binding: Understanding the limitations of
mapping protein surfaces
Heather A Carlson
10:45 - 377 - Applications of 3D-RISM to
structure-based drug design
Jean-François Truchon, Paul Labute.
3:00 - 406 - Designing and unraveling
promiscuous inhibitors against drug-resistant
target mutations
Yang Shen, Mala L Radhkarishnan, Bruce
Tidor.
11:15 - 378 - Water displacement and
conformational shifts in protein-ligand
binding thermodynamics
Michael K. Gilson
3:30 - Intermission
COMP, Emilio Esposito, Scott Wildman
Wednesday, April 10, 2013
3:45 - 407 - How proteins bind macrocycles:
Lessons for the design of macrocyclic
compound libraries for drug discovery
Elizabeth A Villar, Dmitri Beglov, Sandor
Vajda, Adrian Whitty.
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - PM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
4:15 - 408 - Could it be magic? Unusual and
interesting protein-ligand interactions
Martha S Head, Denise Pohlhaus.
Rama Kondru, Sung-Sau So, Vickie Tsui,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
Presiding
1:30 pm - 5:15 pm
4:45 - 409 - Characterization of
sulfotransferase specific metabolism using
dynamic pharmacophores
Christin Rakers, Gerhard Wolber.
COMP, Emilio Esposito, Scott Wildman
Thursday, April 11, 2013
1:30 - 403 - Investigation of the structural
basis for the differential metabolism of
glucocorticoids by CYP3A4 and CYP3A5
enzymes
Kiumars Shahrokh, Garold S Yost, Thomas E
Cheatham III.
Protein-Ligand Interactions: Insights, New
Tools and Applications in Drug Design - AM
Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
2:00 - 404 - G-protein coupled receptors in
virtual screening: Functional fidelity and
selectivity
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Rama Kondru, Sung-Sau So, Vickie Tsui,
Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui,
Presiding
8:30 am - 11:45 am
10:00 - Intermission
8:30 - 438 - Applications of weighted
ensemble molecular dynamics to free energy
landscapes
Sreeja Parameswaran, David Mobley.
10:45 - 442 - Expert protein-ligand interaction
analysis delivered to chemist's desktop
Huifen Chen, Neil R. Taylor, Slaton Lipscomb,
Jeff Blaney.
9:00 - 439 - Annotating protein-ligand
relationships with binding site surface
similarity using Surflex-PSIM
Russell Spitzer, Ann E Cleves, Ajay N Jain.
11:15 - 443 - Structure-based drug design
exploiting dynamic combinatorial chemistry
to identify novel inhibitors for the aspartic
protease endothiapepsin
Anna KH Hirsch
10:15 - 441 - Necessity of clean data: Protein
preparation in the GUI era
Carsten Detering
9:30 - 440 - Identifying binding hot-spots with
molecular interaction networks
Bernd Kuhn, Neil R. Taylor.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Symposia with Abstracts
ACS Chemical Information Division (CINF)
245th ACS National Meeting, Spring 2013
New Orleans, LA (April 7 - 11) CINF Symposia
J. Garritano, Program Chair
[Created Monday Mar 18 2013, Subject to Change]
Sunday, April 7, 2013
inherent in the MLPCN screening set, and
biogenic bias of the set. Our analyses suggest
that MLPCN targets cover biologically
interesting pathway space that is distinct
from established drug targets, but may
include genes whose overly complex protein
interactions may obfuscate pathway effects
and enable therapeutically undesirable sideeffect risks. We find the MLPCN screening set
to be chemically diverse, and it has greater
biogenic bias than comparable collections of
commercially available compounds. Biogenic
enhancements such as incorporation of more
metabolite-like chemotypes are suggested.
Advances in Visualizing and Analyzing
Biomolecular Screening Data - AM Session
Data-Mining Public Bioactivity Data
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan,
Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
8:30 am - 11:50 am
8:30 - Introductory Remarks
9:00 - 2 - New ways to mine disparate
screening data in PubChem
Evan Bolton, [email protected],
PubChem, NCBI / NLM / NIH, United States
8:35 - 1 - Characterizing the diversity and
biological relevance of the MLPCN assay
manifold and screening set
Jun Huan, [email protected], EECS, Univ. of
Kansas, lawrence, ks 66049, United States
PubChem is an open repository for chemical
biology information. PubChem contains ~2.5
million biologically tested substances
(representing 1.8 million unique small
molecules) and ~200 million biological
experiment result outcomes. This large
corpus of information requires innovative
approaches to swiftly find and summarize
desired information. While PubChem has a
number of pre-existing capabilities to mine
biological screening data, such as summary
counts and heat-map style displays, this talk
will detail new innovations that provide
dramatically expanded capabilities to rapidly
The NIH Molecular Libraries Probe Production
Centers Network (MLPCN) aims to remediate
key deficiencies in drug discovery and
chemical biology, through pursuit of
therapeutically feasible but unprofitable drug
targets, undruggable genes of biochemical
interest, and development of chemically
diverse, biologically relevant screening sets.
This paper evaluates the novelty of MLPCN
targets, their propensity for undergoing
modulations of biochemical or therapeutic
relevance, the degree of chemical diversity
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Chemical Information Bulletin Vol. 65(1) Spring 2013
navigate and relate chemical and biological
data within the resource.
provide a rapid development tool to create
content-rich and interactive UIs without
requiring the development of such a data
warehouse. These widgets show commonly
requested PubChem data views, such as 1)
patents associated with a PubChem
compound or substance; 2) bioactivity
outcomes for a PubChem compound,
substance, or bioassay; 3) Literature available
for a compound, substance, or bioassay.
These widgets are easily embedded into your
own web application or HTML pages, and can
also be used to access annotation data from
native desktop and mobile applications. Beta
release available:
http://pubchem.ncbi.nlm.nih.gov/widget/doc
s/widget_help.html.
9:25 - 3 - PubChem DataDicer: A data
warehouse for rapid querying of bioassay
data
Lewis Y Geer, [email protected], Lianyi
Han, Siqian He, Yanli Wang, Evan E Bolton,
Stephen H Bryant. NLM/NCBI, NIH, Bethesda,
Maryland 20894, United States
The amount of publically available bioassay
data has increased to the range of 200M
endpoints. At the same time, this data can be
linked to a large amount of information in a
variety of databases, such as NCBI Gene and
PubChem Compound. The breadth and depth
of this data presents challenges for
researchers attempting to extract useful data
for their research. The PubChem DataDicer
centralizes this information in a single data
warehouse allowing the researcher to rapidly
locate assay endpoints with similar
characteristics, such as shared pathways,
targets and chemical properties, for further
analysis. We have also investigated the
creation of a RESTful web API for
programmatic access to this data warehouse.
10:15 - Intermission
10:35 - 5 - Automated structure-activity
relationship mining: Connecting chemical
structure to biological profiles
Mathias Wawer1,
[email protected], David
Jaramillo1, Kejie Li1, Sigrun Gustafsdottir1,
Vebjorn Ljosa4, Nicole Bodycombe1, Melissa
Parkin3, Katherine Sokolnicki4, Mark-Anthony
Bray4, Ellen Winchester3, George Grant3, Cindy
Hon1, Jeremy Duvall2, Joshua Bittker2, Vlado
Dancik1, Rajiv Narayan5, Aravind
Subramanian5, Wendy Winckler3, Todd
Golub5, Anne Carpenter4, Stuart Schreiber1,
Alykhan Shamji1, Jürgen Bajorath6, Paul
Clemons1. (1) Chemical Biology Program,
Broad Institute, Cambridge, MA 02142,
United States, (2) Chemical Biology Platform,
Broad Institute, United States, (3) Genomics
Platform, Broad Institute, United States, (4)
Imaging Platform, Broad Institute, United
States, (5) Cancer Program, Broad Institute,
United States, (6) Department of Life Science
Informatics, B-IT, LIMES, University of Bonn,
Bonn, Germany
9:50 - 4 - PubChem widgets
Lianyi Han, [email protected], National
Center for Biotechnology Information,
National Institutes of Health, Bethesda, MD
20894, United States
Modern interactive web and mobile
applications for chemistry and biology often
need to integrate information from multiple
resources, such as biochemical analysis,
patents, and publications. This typically
requires an underlying data warehouse
containing billions of chemical and bioactivity
records coupled with web services that
deliver "Asynchronous JavaScript and XML"
(AJAX) and JSONP(or "JSON with padding")
content to applications. PubChem Widgets
Understanding structure-activity relationships
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Chemical Information Bulletin Vol. 65(1) Spring 2013
(SARs) of small molecules is important for the
development of probes and novel therapeutic
agents in chemical biology and drug
discovery. We developed computational
methods to automatically mine and visualize
SARs for small-molecule screening and
profiling data. We applied these methods to
data from novel gene-expression and imaging
assays collected for more than 22,000 small
molecules. The collection contains novel
compounds originating from diversityoriented synthesis (DOS) as well as known
bioactive molecules. The DOS compound
collection covers a diverse chemical space
while including structural analogs and
stereoisomers. We automated the discovery
of rules that connect chemical features of
these compounds to their biological profiles,
allowing us to prioritize groups of compounds
for further study.
inhibitory concentrations, it is possible to
simultaneously cluster together both
compounds with similar bioactivities, and
targets that are modulated by common
compounds. We assert that the result of this
bi-clustering provides an interesting visual
representation of the space of
molecule/target interactions. We have also
shown that Bi-SPE can be used as a
collaborative filtering machine learning
algorithm to accurately predict unknown
compound/target interactions from the ones
present in the training data set.
11:25 - 7 - BioAssay Research Database: A
platform to support the collection,
management, and analysis of chemical
biology data
Rajarshi Guha1, [email protected], David
Lahr2, Joshua Bittker2, Thomas D.Y. Chung3,
Mark Southern7, Simon Chatwin2, Jeremy J
Yang4, Oleg Ursu4, Christian G Bologa4, Tudor
I Oprea4, Eric Dawson5, Shaun R Stauffer5,
Craig W Lindsley5, Uma Vempati6, Hande
Kucuk6, Stephan C Schurer6, Stephen Brudz2,
Paul A Clemons2, Andrea de Souza2, Noel
Southall1, Dac-Trung Nguyen1, John Braisted1,
Tyler Peryea1. (1) NIH Center for Advancing
Translational Science, Rockville, MD 20850,
United States, (2) Broad Institute, Cambridge,
MA 02143, United States, (3) Conrad Prebys
Center for Chemical Genomics, SanfordBurnham Medical Research Institute, La Jolla,
CA 92037, United States, (4) Department of
Internal Medicine, University of New Mexico,
Albuquerque, NM 87131, United States, (5)
Vanderbilt University, Nashville, TN 37232,
United States, (6) University of Miami, Miami,
FL 33101, United States, (7) Scripps Research
Institute, Jupiter, FL 33458, United States
11:00 - 6 - Using the bi-clustering SPE for the
visualization and analysis of massive
amounts of compound-target activity data
Dmitrii Rassokhin1, [email protected],
Dimitris Agrafiotis2, Eric Yang2. (1)
Department of Translational Informatics,
Janssen Pharmaceutical Companies of
Johnson &Johnson, Spring House, 19477-0776
19477-0776, United States, (2) Department of
Neuroscience Informatics, Janssen
Pharmaceutical Companies of Johnson
&Johnson, Spring House, PA 19477-0776,
United States
We have developed an algorithm termed BiClustered Stochastic Proximity Embedding (BiSPE), which is an extension of the SPE
mapping algorithm originally proposed by
Agrafiotis et al., and successfully used it for
the visualization of very large compound
bioactivity data sets. We have shown that
using the compound/target distance metric
derived directly from certain types of
bioactivity measurements, such as enzyme
inhibition constants and the half maximal
The BioAssay Research Database(BARD) was
conceived to enable scientists to effectively
use the National Institutes of Health(NIH)
Molecular Libraries Program(MLP) data. The
project is a collaboration between several
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Chemical Information Bulletin Vol. 65(1) Spring 2013
institutions across the US, and has recently
released an infrastructure that supports
collection and annotation of bioassay
screening data using a well-defined
vocabulary, dissemination of data via web
and desktop clients, and a mechanism to help
develop novel views and analyses of data in
the associated databases. In this
presentation, we describe the design and
implementation of the technical
infrastructure that underlies BARD. We will
highlight contextualization of assay results
(via links to external resources coupled with
full-text indexing) and describe how BARD
functionality can be extended by the
community using plug-ins. As an exemplar of
such community-driven extensions, we will
describe how the BadApple promiscuity
method was integrated into BARD via a plugin
developed at the University of New Mexico.
"Academic Branch Libraries in Changing
Times" (Chandos Publishing, 2011) will
present a short overview of the
transformation of the branch academic
libraries over the years, with a special
emphasis on branch libraries in the science
disciplines.
8:50 - 9 - Library spaces for scientific
computing discovery and learning
Andrea Twiss-Brooks,
[email protected], Division of Science
Libraries, University of Chicago, Chicago, IL
60637, United States
The University of Chicago Library is
committed to creating hospitable physical
and virtual environments for study, teaching,
and research and to collaborating with other
members of the University to enrich research
and learning. The Library has engaged with
various stakeholders to create spaces for
furthering these goals. Collaborations include
a partnership with the Research Computing
Center to create the Data Visualization
Laboratory in The Kathleen A. Zar Room
http://rcc.uchicago.edu/resources/data_visua
lization.html, the creation of a computer
equipped classroom for all University of
Chicago library staff in a former computer lab
area, and planning with various campus units
to create additional technology equipped
classrooms in the John Crerar Library.
Currently existing spaces have already been
used to host a number of workshops,
research seminars, training sessions, and
other events. Descriptions of the
collaborations, facilities and plans will be
provided.
Sunday, April 7, 2013
Library Cafes, Intellectual Commons and
Virtual Services, Oh My! Charting New
Routes for Users into Research Libraries - AM
Session Transforming Libraries
Morial Convention Center
Room: 350
Cosponsored by CHED
Leah Solla, Olivia Bautista Sparks, Teri Vogel,
Organizers
Leah Solla, Teri Vogel, Presiding
8:20 am - 11:45 am
8:20 - Introductory Remarks
8:25 - 8 - Transformation of academic branch
libraries
Nevenka Zdravkovska, [email protected],
Engineering and Physical Sciences Library,
University of Maryland, College Park, MD
20742, United States
9:15 - 10 - Heart of the university or how to
stay stuck in the middle with you
Susanne J Redalje, [email protected], Lauren
Ray. Libraries, University of Washington,
Seattle, Washington 98195-2900, United
States
Nevenka Zdravkovska, author of the book
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Chemical Information Bulletin Vol. 65(1) Spring 2013
previously organized around (and confined
by) the geographic layout of our campus
libraries. With the benefit of two years' worth
of hindsight, this presentation highlights a
few examples of how a more agile
organizational model has resulted in new
opportunities-- and new challenges-- for
serving our communities and for developing
liaison librarian competencies.
Only rarely do librarians consider their users
clown or jokers as suggested by the Stealers
Wheel. We do, however, want to stay stuck in
the middle with them and continue to be as
relevant to their research and educational
needs as we were when Harvard University
President Charles William Eliott considered
the Library as the heart of the University.
Budgetary issues, technological
advancements and new ways of teaching and
communicating make this a challenge. Like
many Universities, the University of
Washington is involved in several initiatives to
address this problem. In the fall of 2010, the
Research Commons was opened in the space
formerly housing the Natural Sciences branch
library. This is the first of several such spaces
designed to connect with user individually or
as groups. It provides flexible spacing and
technology to help meet users research,
teaching and learning needs. The Libraries has
worked closely with the Graduate College to
provide relevant programming aimed at
graduate students. One particularly successful
program includes lightning talks based on an
interdisciplinary topic allowing graduate
students experience in presenting research
and get feedback on their presentations.
Assessment of the space shows users are very
happy with it and also suggests directions for
the future.
10:05 - Intermission
10:20 - 12 - Holistic approaches to service:
Connecting researchers to libraries through
relationship building
Kiyomi D. Deards, [email protected],
University of Nebraska-Lincoln, Lincoln, NE
68588-4100, United States
Flexibility and a focus on the needs of library
users is a frequent refrain in today's rapidly
changing society. How are those needs
determined? How are users approached for
input? Do you dislike knocking on doors when
you're not expected? Come discuss
opportunities for informal interactions that
lead to collaborations, acquisitions of
resources, instructional invitations and more.
The importance of relationship building and
quality of contacts versus quantity of contacts
will also be explored.
10:45 - 13 - Ask for research alterations:
Emerge with a custom fit
Jill E Wilson, [email protected], Leah R
McEwen. Engineering, Mathematics, and
Physical Sciences Libraries, Cornell University,
Ithaca, NY 14853, United States
9:40 - 11 - From traditional library
organization to functional structure: How
does it benefit library users?
Erja Kajosalo, [email protected], Libraries,
Massachusetts Institute of Technology,
Cambridge, MA 02139, United States
Libraries offer suites of collections, resources
and services which can appear to be one size
fits all, ready-to-wear approaches to doing
research. Users “shop” library websites and
services for information to discover the best
“fit” their research needs. Often, after many
tryings-on, our researchers push back with
In 2010, MIT Libraries underwent a
reorganization that changed the way subject
librarians cooperated to meet information
needs across the Institute. Interdisciplinary
"communities of practice" replaced a more
traditional reporting structure that was
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Chemical Information Bulletin Vol. 65(1) Spring 2013
sentiments such as “Why can't I just get what
I need to get from one place?” or “I just can't
find what I am looking for right away.”
Librarians at Cornell's Physical Sciences
Library demonstrate the impact their libraries
have on users experience with the notion that
we custom tailor for each unique need and
provide alterations to the cycle of scholarly
communication for best results. We respond
with tailored outreach and services including
specialized finding tools, an interactive virtual
presence and custom workshops on
professional development through working
partnerships with our graduate students.
Research snags may appear with first fitting;
however our strength is not just the
collections we offer, but how we fit them into
our patrons' lives.
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan,
Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
2:00 pm - 5:15 pm
2:00 - 15 - 3D phylogenetic trees for
visualization and analysis of complex
datasets
Ruben Abagyan1,2, [email protected],
Eugene Raush2, Maxim Totrov2. (1) Skaggs
School of Pharmacy &Pharmaceutical
Sciences, University of California San Diego, La
Jolla, CA 92093, United States, (2) MolSoft,
San Diego, CA 92121, United States
11:10 - 14 - Let's work together: ACS
Publications author outreach initiatives and
opportunities for libraries
Sara Rouhi, [email protected], Publications
Division, American Chemical Society,
Washington, DC 20036, United States
Visualizing a large number of objects defined
by a distance matrix or as points in a
multidimensional space efficiently has always
been challenging. Three main methods have
been developed: showing the objects as
phylogenetic trees in two dimensions,
showing the objects as network diagrams,
and showing three principal coordinates (or
just three arbitrarily chosen parameters from
multidimensional coordinates). Here we
present a new method which combines the
phylogenetic trees with the placement of the
objects in three dimensional space. The new
method has been implemented in the ICM
suite of programs from MolSoft as an
interactive object which is dynamically linked
with the underlying data. The new three
dimensional trees are efficient in visualizing
complex relationships between large
collections of objects of any nature once the
distance matrix can be established. We
illustrate this representation on a large
collection of chemicals, screening data and
biological sequences.
The changing digital landscape offers new
opportunities for libraries and publishers to
reach out to users in new ways. ACS
Publications will share a number of ongoing
initiatives that libraries can use to help
educate their patrons on topics ranging from
ethics and copyright in scholarly publishing to
manuscript composition and the process of
peer-review. We'll also share our ongoing
engagement efforts with young scientists
through the ACS Summer Institute. Also look
for an update on the ACS Style Guide Online
and the debut of a new scholarly research
tool from the ACS.
Sunday, April 7, 2013
Advances in Visualizing and Analyzing
Biomolecular Screening Data - PM Session
Tools, Techniques, Platforms and Software
2:25 - 16 - On-line graph mining and
visualization of protein-ligand interactome
68
Chemical Information Bulletin Vol. 65(1) Spring 2013
Clara Ng1, [email protected], Lei
Xie1,2, [email protected]. (1)
Department of Computer Science, City
University of New York, New York, NY, United
States, (2) Graduate Center, City University of
New York, New York, NY, United States
creation of large combinatorial libraries
whose members (sometimes over a billion!)
are encoded by a unique combination of DNA
tags. Binders to a molecular target are
selected from these libraries and identified
using next-generation DNA sequencing. We
have developed a platform for translating
sequence data back to the encoded chemical
warhead, detecting features that are enriched
in the selection, and summarizing and
annotating the selection experiment. Each
week our platform processes over 100 million
DNA sequences - larger than the entire
human genome. Data visualization is
integrated into the TIBCO Spotfire platform,
allowing scientists to view summaries of the
large data sets, determine the most
important chemical space, and then drill
down to specific results to prioritize
compounds for synthesis and assays. We will
describe method details and present
examples to highlight our analysis and
visualization tools.
Recent high-throughput screens have
generated a lot of protein-ligand interaction
data; for example, over one million
compounds are associated with the 4422
proteins in ChEMBL. Recent attempts to mine
and visualize this large protein-ligand
interaction dataset have mapped chemicals
into a high-dimensional feature space and
visualized it using dimensionality reduction
techniques. We propose a different approach
to exploring the protein-ligand interactome
efficiently, effectively, and intuitively. We link
all chemicals and targets into an all-against-all
chemical similarity network and target
similarity network, respectively. The networks
are connected as a bipartite graph through
protein-ligand interactions. Efficient graph
clustering and mining algorithms are applied
to identify chemical and protein patterns
underlying binding promiscuity and
specificity. Although the chemical/protein
similarity network is computationally
intensive, it need only be built once and
updated regularly. As demonstrated in case
studies for anti-infectious drug discovery, our
method may facilitate drug repurposing, sideeffect prediction, and polypharmacology drug
design.
3:15 - Intermission
3:35 - 18 - Exploring the chemical space of
screening results
Ed Champness, [email protected], Matt
Segall, Chris Leeding, James Chisholm,
Iskander Yusof, Hector Martinez, Nick Foster.
Optibrium Ltd., Cambridge, United Kingdom
When faced with the results from a screening
campaign it is essential to use this data to
quickly focus on the best chemistries for
progression. In this presentation we will
describe two techniques for visualising a
'chemical space' to guide this exploration. We
will demonstrate how these can be used to
identify activity 'hotspots' and focus on these
for detailed analysis of structure-activity
relationships. This approach can also help to
spot singletons and outliers that may
represent false positives or negatives for
further investigation. Furthermore, it is well
2:50 - 17 - Encoded Library Technology data
analysis: Finding the grain of sand you want
without getting a sunburn
Kenneth E Lind, [email protected], Neil
R Carlson, Ninad V Prabhu, Jeff A Messer.
MDR Boston, GlaxoSmithKline, Waltham, MA
02451, United States
Encoded Library Technology (ELT) is a part of
GSK's integrated Hit ID strategy. ELT involves
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Chemical Information Bulletin Vol. 65(1) Spring 2013
understood that high quality chemistry will
have not only good activity, but also
appropriate absorption, distribution,
metabolism, elimination and toxicity (ADMET)
properties. We will show how data from
multiple sources can be combined to select
compounds for further study with an
appropriate balance of activity, ADMET
properties and structural diversity to mitigate
downstream risk.
With the growing number of academic
laboratories conducting high-throughput
screening (HTS) comes the need for accessible
and easily customizable software capable of
visualizing and analyzing HTS results. Herein,
we report on the development of the HTS
Navigator software (freely available for
academia). It allows loading and processing of
output files for both individual and batches of
plates from different readers' formats,
visualization of the overall heat map colored
by activity, automatic detection of hits as well
as compounds with mono- and dualselectivity for screened targets, and different
types of baseline corrections. HTS Navigator
includes basic cheminformatics capabilities
such as chemical structure storage and
visualization, fast similarity search and
neighborhood analysis for retrieved hits,
hierarchical clustering in both chemistry and
activity spaces, and the detection of activity
cliffs. The Navigator is coupled to the
ADDAGRA software for visualizing compound
clusters and outliers in both multidimensional
chemistry and HTS spaces.
4:00 - 19 - How to highlight hits: Advances in
visual data analytics tools for HTS data
Jesse A. Gordon,
[email protected], Jess Sager.
Application Science, Dotmatics, Ltd., Woburn,
MA 01801, United States
We face a huge dataset from a screening run
and we want to analyze the results to pick
compounds for the next screening run. How
do we sift through the millions of data points
to figure out which are meaningful hits, and
then organize those hits into a database from
which we can intelligently predict good
prospects for the next screening run? We face
a series of challenges in HTS data analysis
which will be outlined in this presentation
followed by solutions offered through
modern chemoinformatics and visual data
analytics tools. We look at the difference
between the "Old Way" -- grid after grid in
Excel with manual calculations -- and the
"New Way" -- clicking on visually distinctive
points highlighted in red on automaticallygenerated curves.
4:50 - 21 - Integrating design, analysis, and
visualization into the drug discovery
workflow
W. Patrick P. Walters1,
[email protected], Carlos Faerman1,
Jonathan Weiss1, Xiaodan Zhang1, Roslyn
Potter1, Jun Feng1, Guy Bemis1, Susan
Roberts2, Jason Yuen2, Trevor Kramer2,
Jonathan Christopher3, Jeff Orr3, Brian
Goldman1. (1) Computational Sciences, Vertex
Pharmaceuticals, Cambridge, MA 02139,
United States, (2) Global Information Services,
Vertex Pharmaceuticals, Cambridge, MA
02139, United States, (3) Global Information
Services, Vertex Pharmaceuticals, San Diego,
CA 92121, United States
4:25 - 20 - Integrated cheminformatics
software for visualizing and analyzing highthroughput screening data
Denis Fourches, [email protected],
Alexander Tropsha. Laboratory for Molecular
Modeling, Division of Medicinal Chemistry and
Natural Products, University of North
Carolina, Chapel Hill, NC 27599, United States
Drug discovery is a complex process that
involves the simultaneous optimization of
multiple parameters. Effective discovery
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Chemical Information Bulletin Vol. 65(1) Spring 2013
teams must be able to analyze data, identify
trends, and decide on a direction for
compound optimization. This analysis
typically requires the synthesis of not only
internal data, but also information culled
from external sources such as patents and
papers. Many informatics systems provide the
ability to query internal data, but few can
integrate design tools with a combined
analysis of internal and external data. Rather
than simply combining all of the data into a
single data warehouse, we have used facilities
such as application programming
interfaces(APIs) to create links to a wide array
of relevant external sources. This
presentation will use a few case studies to
present some of our recent work on a unified
informatics infrastructure that allows facile
access to internal data as well as a variety of
literature sources.
(CCDC) compiles the world's repository of
small molecule organic and organometallic
crystal structures, known as the Cambridge
Structural Database (CSD). Containing over
600,000 X-ray diffraction analyses, the CSD is
a unique resource of invaluable structural
information. We have developed and licence
a comprehensive range of locally installed
desktop tools that enable the database to
interrogated and the results visualised and
analysed, allowing our users to make
maximum benefit of the data. This talk will
summarise the changes we are making in
response to changing user requirements and
technologies, both in terms of how the data
are accessed and in terms of the underlying
structure of the database.
3:00 - 23 - ChemEd DL WikiHyperGlossary: A
social semantic information literacy service
for digital documents
Robert E. Belford1, [email protected], Dan
Berleant2, Michael A. Bauer2, Jon L. Holmes3,
John W. Moore3. (1) Department of
Chemistry, University of Arkansas at Little
Rock, Little Rock, AR 72204, United States, (2)
Department of Information Science, University
of Arkansas at Little Rock, Little Rock, AR
72204, United States, (3) Department of
Chemistry, University of Wisconsin-Madison,
Madison, WI, United States
Sunday, April 7, 2013
Library Cafes, Intellectual Commons and
Virtual Services, Oh My! Charting New
Routes for Users into Research Libraries - PM
Session Online Tools
Morial Convention Center
Room: 350
Cosponsored by CHED, COMP
Leah Solla, Teri Vogel, Olivia Bautista Sparks,
Organizers
Leah Solla, Teri Vogel, Presiding
2:30 pm - 5:00 pm
ChemEd DL WikiHyperGlossary (WHG)
automates the markup of digital text
documents and web pages, inserting
hyperlinks pointing to an associated glossary
and returning the content in a JavaScript
overlay. Both editable and non-editable
definitions can be returned, and a glossary
architecture designed to enhance reading
comprehension by coupling social to
canonical definitions will be presented. The
overlay also connects documents to
databases (UniProtKB, Models 360), with tabs
going to search services (ChemSpider) and
software agents like Jmol and JChemPaint.
2:30 - Introductory Remarks
2:35 - 22 - Cambridge Structural Database:
Moving with the times
Susan Henderson,
[email protected], Ian J Bruno.
CCDC, Cambridge, Cambridgeshire CB2 1EZ,
United Kingdom
The Cambridge Crystallographic Data Centre
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Chemical Information Bulletin Vol. 65(1) Spring 2013
McEwen. Engineering, Mathematics, and
Physical Sciences Libraries, Cornell University,
Ithaca, NY 14853, United States
The later enables researchers to create new
search tabs based on their edits, which leads
to a molecular-editor enabled knowledge
framework targeting the effects of the
researcher's edits. Digital archives like Project
Gutenberg enable the WHG to introduce
social-semantic features into historic
documents, thereby directly connecting past
works of science like Antoine Lavoisier's
“Elements of Chemistry” to modern
informatics resources. The WHG development
site is http://hyperglossary.org/.
Keeping up with physical scientists demands
that more online information be discoverable.
The Physical Sciences eLibrary at Cornell
blends the most crucial components of the
brick-and-mortar model with forward looking
developments in the greater discovery
landscape to build new tools for faceted
browsing and locating specific material types.
We are leveraging new infrastructure that
allows subject librarians to layer annotations
and additional metadata on top of library
catalog records. We collaborate closely with
the researchers and scientists in an iterative
development cycle to build a responsive
eLibrary that enables us to go beyond
traditional services. In this talk we will
provide an overview of our process and
discuss how we are translating the delivery
mechanisms of the library web presence at
Cornell.
3:25 - 24 - Navigating scientific resources
using wiki-based resources
Antony J Williams1, [email protected], Valery
Tkachenko1, Alexey Pshenichnov1, Sean Ekins3,
Aileen Day2, Martin Walker4. (1)
Cheminformatics, Royal Society of Chemistry,
Wake Forest, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom, (3)
Collaborations in Chemistry, Fuquay Varina,
NC, United States, (4) Potsdam University,
Potsdam, NY, United States
Sunday, April 7, 2013
There is an overwhelming number of new
resources for chemistry that would likely
benefit both librarians and students in terms
of improving access to data and information.
While commercial solutions provided by an
institution may be the primary resources
there is now an enormous range of online
tools, databases, resources, apps for mobile
devices and, increasingly, wikis. This
presentation will provide an overview of how
wiki-based resources for scientists are
developing and will introduce a number of
developing wikis. These include wikis that are
being used to teach chemistry to students as
well as to source information about scientists,
scientific databases and mobile apps.
CINF Scholarship for Scientific Excellence EVE Session
Morial Convention Center
Room: 343
Guenter Grethe, Organizers
6:30 pm - 8:30 pm
26 - iBIOMES: Managing and sharing large
biomolecular simulation datasets in a
distributed environment with iRODS
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3. (1)
Department of Biomedical Informatics,
University of Utah, Salt Lake City, Utah 84112,
United States, (2) Department of Medicinal
Chemistry, University of Utah, Salt Lake City,
Utah 84112, United States, (3) Center for
High-Performance Computing, University of
3:50 - 25 - CuLLR me collaboration: Models
and tools for user-driven eLibraries
Dianne Dietrich, [email protected], Leah R
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Utah, Salt Lake City, Utah 84112, United
States
27 - Probing the substrate selectivity of the
serotonin and dopamine transporter using
structure based techniques
Amir Seddik1, [email protected],
Harald H. Sitte2, Gerhard F. Ecker1. (1)
Department of Medicinal Chemistry,
University of Vienna, Vienna, Austria, (2)
Department of Pharmacology, Medical
University of Vienna, Vienna, Austria
During this presentation we will introduce the
architecture of iBIOMES (Integrated
BIOMolEcular Simulations), a distributed
system for biomolecular simulation data
management allowing storage and indexing
of large datasets generated by Molecular
Dynamics (MD) simulations, along with ab
initio calculation results. The system
architecture is based on iRODS, a data
handling system developed by RENCI, and
influenced by the experience gained from the
Storage Resource Broker (SRB) system. iRODS
provides the tools to register, move, and
lookup files that are distributed over the
network and stored in different types of disk
(e.g. HPC servers, files servers, archive tapes).
Registered files can be queried and retrieved
based on system or user-defined metadata.
We created customized interfaces on top of
iRODS to facilitate the data registration
process for biomolecular simulation datasets
(e.g. AMBER, Gaussian). The process is highly
customizable through XML descriptors,
enabling users to choose which piece of data
should be displayed to summarize the
registered experiments. Data registration
does not require physical transfer of the data,
which makes it a great solution for
researchers who want to expose existing
datasets. Input and output files can be made
available for download within a collaborative
network to allow replication of results or
comparison between methods (e.g. different
force-fields). Finally data summarization and
management are facilitated through a rich
web interface that offers different
visualization components for 3D structures
and analysis data (e.g. time series plots,
heatmaps). iBIOMES represents one of the
first efforts to create an infrastructure for
researchers to manage their MD data locally,
expose their data to the community, and
create collaborative networks.
Previous studies revealed that (S)fenfluramine (SFF) shows high selectivity for
SERT over DAT. In this study, this compound is
therefore used as probe ligand to explore the
molecular basis of substrate selectivity at
these two neurotransmitter transporters. A
set of nine high affinity phenylethylamines
(PEAs) was docked into the substrate binding
site of a SERT homology model. Energy
minimization, common scaffold clustering and
consensus scoring resulted in a final pose
which was superposed with the highestranked SFF-DAT complex. Results showed a
similar pose in both transporters, whereby
SFF's CF3 group was placed inside a pocket.
SFF's low affinity for DAT could thus not be
explained by steric hindrance. However, local
alignment indicates a more lipophilic SERT
pocket and a halogen bond donating Thr439,
both of which might explain SERT selectivity
of (S)-fenfluramine. We acknowledge
financial support provided by the Austrian
Science Fund, grants F03502 and W1232.
28 - New cheminformatics microscopes:
Combining semantic web technologies,
cheminformatical representations, and
chemometrics for understanding and
predicting chemical and biological properties
Egon L Willighagen,
[email protected],
Department of Bioinformatics - BiGCaT,
Maastricht University, Maastricht, The
Netherlands
Cheminformatics is a computational
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Chemical Information Bulletin Vol. 65(1) Spring 2013
microscopy with which we study chemical
properties. My research develops new
microscopes based on cheminformatics, using
semantic web and chemometrics
technologies. This resulted in and contributed
to many computational methods to handle
chemical structures and predict their
chemical, physical, and biological properties.
These methods include computational
software like the Chemistry Development Kit,
visualization tools like Jmol, JChemPaint, and
Bioclipse, and information retrieval
technologies like OSCAR4, as well as data
exchange standards like the Chemical Markup
Language, the CHEMINF ontology, and other
semantic solution aimed at reducing
information loss, and new public chemical
knowledge based, such as the Blue Obelisk
Data Repository and the NanoWiki with
toxicological properties of nanomaterials.
These and other tools have used in the
combination with statistical and machine
learning methods to predict properties of
various chemical properties, showing the
importance of statistical and visual validation
of found patterns.
antagonists, combining ligand- and structurebased design. First, we performed a shapeand feature-based similarity search against
commercially available compound collections,
using TLR2 agonists from literature and two
TLR2 antagonists previously identified inhouse as query structures. Second, molecular
interaction fields (MIFs) of the TLR2 binding
site were calculated to derive a structurebased 3D pharmacophore that was then used
for virtual screening. A selection of virtual
screening hits was biologically tested in a cellbased assay for TLR2 inhibition, leading to
several compounds with antagonistic activity
(IC50) in the micromolar range.
Monday, April 8, 2013
Advances in Visualizing and Analyzing
Biomolecular Screening Data - AM Session
Experimental Insights, Case Studies, and
New Methods
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan,
Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
8:30 am - 11:55 am
29 - Discovery of TLR2 antagonists by virtual
screening
Manuela S Murgueitio1, [email protected], Sandra Santos-Sierra2, Gerhard
Wolber1. (1) Institute of Pharmacy,
Pharmaceutical Chemistry, Freie Universität
Berlin, Berlin, Berlin 14195, Germany, (2)
Institute of Clinical Pharmacology,
Medizinische Universität Innsbruck, Innsbruck,
Tirol A-6020, Austria
8:30 - Introductory Remarks
8:35 - 30 - Dispensing processes profoundly
impact biological assays and computational
and statistical analyses
Sean Ekins1, [email protected], Joe
Olechno2, Antony J Williams3. (1)
Collaborations in Chemistry, Fuquay-Varina,
NC 27526, United States, (2) Labcyte Inc,
Sunnyvale, CA 94089, United States, (3) Royal
Society of Chemistry, Wake Forest, NC 27587,
United States
Toll-like receptors (TLRs) represent the first
barrier in innate immune response and act as
key players in the development of chronic
inflammatory and autoimmune diseases.
Thus, interest for identifying small organic
molecules modulating TLRs has risen. In this
study we present a virtual screening approach
for the identification of novel TLR2
Dispensing processes profoundly influence
estimates of biological activity of compounds.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
In this study using published inhibitor data for
the tyrosine kinase EphB4, we show that IC50
values obtained via disposable tip-based
serial dilution and dispensing versus acoustic
dispensing differ by orders of magnitude with
no correlation or ranking of datasets.
Importantly, the computed EphB4
pharmacophores derived from this data differ
for each dataset. Acoustic dispensing
correctly highlights multiple hydrophobic
features in the pharmacophore and correlates
with calculated LogP values. Significantly, the
acoustic dispensing-derived pharmacophore
correctly identified active compounds in a
test set. The subsequent analysis of crystal
structures for other published EphB4
inhibitors and automated development of
pharmacophores, indicated they were
comparable to those developed with acoustic
dispensing data. In short, dispensing
processes are another important source of
error in high-throughput screening that
impacts computational and statistical
analyses. These findings have far-reaching
implications in biological research and in drug
discovery.
positives from primary screens. An Inhibition
Frequency Index (IFI) has been defined as a
measure of promiscuity of individual
compounds in HTS primary assays based upon
activities tabulated over time in GSK's
exhaustive screening assay tables. In this talk,
we will present our analysis of the IFI profile
across the GSK HTS collection. We will
characterize the IFI profile with respect to
desired physical properties, will discuss
obvious substructures that may be less
attractive as starting points, and will describe
new classes of nuisance compounds revealed
by our IFI analysis. In addition, we will
examine the IFI of promiscuity filters
described in the literature. There are many
reasons why any particular molecule might
display promiscuity: physical properties of the
compound, properties of the target or target
class, details of the assay and the assay
technology and methodology. All of these
factors must be considered when deciding
whether to remove or retain a compound in a
curated HTS collection.
9:25 - 32 - Analyzing screening and similarity
searching outcome in light of multiple
approaches to the same target
Tina Garyantes, [email protected],
MAXSAR Biopharma, Warren, NJ 07059,
United States
9:00 - 31 - On the compound annotation and
cleaning the GSK screening collection
initiative: The utility of an Inhibition
Frequency Index (IFI)
Subhas J Chakravorty,
[email protected], James A
Chan, Juan Luengo, Nicole M Greenwood,
Ioana Popa-Burke, Ricardo Macarron. CSC,
Sample Technologies, GSK, Upper Providence,
PA 19426, United States
Traditional candidate discovery tends to be a
linear process, with sequential optimization
of compound parameters and hand-offs
between teams, starting with a very basic
analysis of primary screening data. Often the
“best” series as identified by early assays are
not the “best” series for late optimization.
This talk will ask how we can improve lead
series and potentially identify drug candidates
by improved analysis early in the lead ID
process. We will look at the value of and
methods for analyzing multiple assays in
parallel. An example of parallel optimization
will be discussed where a phenotypic assay
High throughput screening (HTS) constitutes a
critical tool for the identification of lead
molecules from primary screening assays for
novel targets. GlaxoSmithKline (GSK) has
continuously invested in the development
and curation of its HTS collection to maximize
the number of quality starting points for drug
discovery and reduce the number of false
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Chemical Information Bulletin Vol. 65(1) Spring 2013
and a targeted assay were run in parallel.
Data will be shown that supports the
conclusion that running the parallel assays
directs the team into different chemical space
than a more traditional sequential approach.
In addition, a novel method for analyzing the
success of series expansion will be presented
in this context.
securely enable collaborative analysis that
can yield better insight into screening
technology as a whole.
10:35 - 34 - Characterization and
visualization of compound combination
responses in a high throughout setting
Rajarshi Guha, [email protected], Lesley
Mathews, John Keller, Paul Shinn, Craig
Thomas, Anton Simeonov, Marc Ferrar.
Preclinical Innovation, NIH Center for
Advancing Translational Science, Rockville,
MD 20850, United States
9:50 - Intermission
10:10 - 33 - Sharing chemical information
from screens without revealing structures
S. Joshua J. Swamidass1,
[email protected], Matthew Matlock1,
Dimitris K. Agrafiotis2. (1) Pathology and
Immunology, Washington University, St Louis,
Missouri 63108, United States, (2) Johnson
&Johnson Pharmaceutical Research
&Development, LLC, Spring House,
Pennsylvania 19477, United States
Many disease treatments make use of a single
therapeutic agent. However, single agent
therapies often produce unwanted sideeffects and resistance. Combination therapies
have been developed as a means to reduce
side effects and avoid resistance, and are now
successfully applied in diseases such as a
cancer, AIDs and malaria. We have recently
developed a high-throughput screening
platform to test pairwise compound
combinations, which can rapidly and
systematically identify additive, synergistic
and antagonistic drug combinations. This
approach can easily generate hundreds of
dose response matrices in a single study and
can increase significantly when applied to
multiple cell lines. We will present some
methods to numerically compare
combinations in terms of their response
matrices, and visualize combination response
comparisons within and across multiple cell
lines. We will also describe how these
techniques can be used to investigate
putative polypharmacological effects that
play a role in compound combination
responses.
We propose a new, secure method of sharing
useful chemical information from smallmolecule screens, without revealing complete
structures of the screen's molecules.
Recently, several groups have developed and
published new methods of analyzing
screening data, including advanced hitpicking, economic optimization, and
visualizations. Applying these methods to
private screening data requires strategies to
share data without revealing chemical
structures. This problem has been previously
examined in the ADME prediction context,
and mostly dismissed as impossible. In
contrast, we present a new strategy for
encoding molecules---based on anonymized
scaffold networks---that seems to safely share
enough chemical information to be useful in
analyzing screening data, while also
sufficiently blinding chemical structures. We
present method details, and analyses of
useful information conveyed and structure
security. This approach enables sharing
screening data across institutions, and may
11:00 - 35 - Characterizing activity
landscapes using network-like similarity
graphs to mine antibacterial data
Veerabahu Shanmugasundaram1,
[email protected],
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Steven Heck1, Justin Montgomery1, Preeti
Iyer2, Dilyana Dimova2, Jürgen Bajorath2. (1)
WorldWide Medicinal Chemistry, Pfizer,
Groton, CT 06349, United States, (2) Life
Science Informatics, University of Bonn, Bonn,
Germany
potential leads is a critical part of early stage
therapeutic discovery. Often, this amounts to
distilling thousands of HTS hits into a small
number of manageable candidate series (or
singletons in some cases) for lead
optimization. While the process is fairly
straightforward, the tools involved can range
anywhere from ad-hoc scripts to custom built
solutions. We will describe methods that take
a set of suitable seed compounds (e.g., the
result of activity selection), extract a set of
relevant scaffolds, and place the scaffolds in
the context of high-quality external data
sources. We couple the scaffold driven
analytics with visualizations of scaffold
structural properties and associated activities
that allow efficient and intuitive exploration
of candidate series. We will finally describe a
software tool that implements these methods
and highlight its utility on HTS data from the
Molecular Libraries Program.
Understanding structure-activity
relationships(SAR) of a set of bioactive
compounds is key to medicinal chemistry
design. Computational techniques like
statistical, pharmacophore and structurebased modeling can provide insights into SAR,
but can also be misled by false assumptions.
For example, one common assumption is that
a series of similar compounds has a common
binding mode or mechanism of action. Other
assumptions include additivity of SAR from
systematic changes, and the similarity
principle: “similar molecules have similar
biological effect”. Characterizing activity
landscapes and early detection of activity
cliffs are crucial to understanding global and
local SAR characteristics, critical for ligandbased virtual screening or lead-optimization
campaigns. Further, in data-sets with a wealth
of historical information, visual examination
of SAR could provide novel insights and reveal
new directions. We adapted Network-like
similarity graphs(NSGs, Bajorath and coworkers) to mine a Pfizer antibacterial dataset, and compare and contrast NSG-based
visual data-mining results with a few
traditional approaches.
11:50 - Concluding Remarks
Monday, April 8, 2013
Scholarly Communication: New Models, New
Media, New Metrics - AM Session
Morial Convention Center
Room: 350
David Martinsen, William Town, Colin
Batchelor, Organizers
David Martinsen, Presiding
8:10 am - 11:30 am
11:25 - 36 - From hits to leads: Data
visualization of chemical scaffolds beyond
traditional SAR exploration
Tyler Peryea, [email protected], John
Braisted, Ajit Jadhav, Rajarshi Guha, Noel
Southall, Dac-Trung Nguyen. National Center
for Advancing Translational Sciences, Division
of Preclinical Innovation, Rockville, Maryland
20850, United States
8:10 - Introductory Remarks
8:15 - 37 - Evolution of ACS DivCHED CCCE
ConfChem: Gopher servers to the social
semantic web
Robert E Belford1, [email protected], Nitin
Agarwal2, Steven Leimberg2, Jon L. Holmes3.
(1) Department of Chemistry, University of
Arkansas at Little Rock, Little Rock, AR 72204,
United States, (2) Department of Information
Turning hits from an HTS campaign into
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Science, University of Arkansas at Little Rock,
Little Rock, AR 72204, United States, (3)
Department of Chemistry, University of
Wisconsin-Madison, Madison, WI, United
States
compound database, ChemSpider. In this talk
we will survey our recent efforts to extract all
kinds of data - chemical structures,
experimental and bibliographic data - from
both our backfile and frontfile. We will also
discuss our future work to extract chemical
reactions to host in our ChemSpider
Reactions database and will discuss the
potential applications of optical structure
recognition technologies for converting
structure images to structures as well as using
similar techniques to convert experimental
spectral data into interactive data formats. A
key aspect of this project is the delivery of a
crowdsourcing platform for the interactive
annotation and validation of the extracted
data.
2013 is the 20th anniversary of the online
ConfChem conferences run by the ACS
DivCHED Committee on Computers in
Chemical Education (CCCE). This may be the
oldest online conference in the chemical
sciences. A brief history of ConfChem's
evolution from ASCII text files being discussed
over a listserver to the current platform will
be provided. Archiving ConfChems and
Newsletters has been a challenge for the
CCCE. We will report on a project using the
Drupal content management system to tackle
this problem, while enhancing discovery
within the archives by connecting past and
present conferences through a socially
generated tag filtration process, that bundles
individual ConfChem and Newsletter papers
along a variety of folksonomy defined
themes. The folksonomy will lend a
knowledge framework to facilitate discovery
and innovation, enabling ConfChem to make
the leap from Web 2.0 to Web 3.0, and
function as a scholarly communication within
the social-semantic web paradigm.
9:15 - 39 - NIST-journal cooperation to
improve the quality of published
experimental data: Pre-acceptance
evaluation and on-line tools
Robert D. Chirico1, [email protected],
Michael Frenkel1, Joseph W. Magee1, Vladimir
V. Diky1, Kenneth Kroenlein1, Chris D. Muzny1,
Andrei F. Kazakov1, Ilmutdin M. Abdulagatov1,
Gary R. Hardin1, Theodoor W. de Loos2, John
P. O'Connell3, Clare McCabe4, Joan F.
Brennecke5, Paul M. Mathias6, Anthony R. H.
Goodwin7, Jiangtao Wu8, Kenneth N. Marsh9,
Ronald D. Weir10, William E. Acree, Jr.11, Agilio
Pádua12, W. M. (Mickey) Haynes1, Daniel G.
Friend1, Andreas Mandelis13, Vicente Rives14,
Christoph Schick15, Sergey Vyazovkin16, Ella
Chen17. (1) Applied Chemicals and Materials
Division, National Institute of Standards and
Technology, Boulder, Colorado, United States,
(2) Department of Process and Energy, Delft
University of Technology, Delft, The
Netherlands, (3) Department of Chemical
Engineering, University of Virginia,
Charlottesville, Virginia, United States, (4)
Department of Chemical and Biomolecular
Engineering and Department of Chemistry,
Vanderbilt University, Nashville, Tennessee,
United States, (5) Department of Chemical
8:45 - 38 - Data enhancing the RSC Archive
Colin Batchelor1, [email protected], Ken
Karapetyan2, Alexey Pshenichnov2, David
Sharpe1, Jon Steele1, Valery Tkachenko2,
Antony Williams2. (1) Royal Society of
Chemistry, Cambridge, United Kingdom, (2)
Royal Society of Chemistry, Wake Forest,
North Carolina 27587, United States
The Royal Society of Chemistry has an archive
of published journals and books stretching
back to 1841. In the past decade we have
digitized this archive and semantically
enriched our frontfile data with chemical
structures linked to our free online chemical
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Chemical Information Bulletin Vol. 65(1) Spring 2013
and Biomolecular Engineering, University of
Notre Dame, Notre Dame, Indiana, United
States, (6) Fluor Corporation, Aliso Viejo,
California, United States, (7) Schlumberger
Technology Corporation, Sugar Land, Texas,
United States, (8) Center for Thermal and
Fluid Science, Xi’an Jiaotong University, Xian,
Shaanxi, China, (9) School of Mechanical and
Chemical Engineering, University of Western
Australia, Crawley, Australia, (10) Department
of Chemistry and Chemical Engineering, Royal
Military College of Canada, Kingston, Ontario,
Canada, (11) Department of Chemistry,
University of North Texas, Denton, Texas,
United States, (12) Laboratoire
Thermodynamique et Interactions
Moléculaires, Université Blaise Pascal and
CNRS, Clermont-Ferrand, France, (13) Faculty
of Applied Science and Engineering, University
of Toronto, Toronto, Ontario, Canada, (14)
Departamento de Quimica Inorganica,
Universidad de Salamanca, Salamanca, Spain,
(15) Institute of Physics, Universität Rostock,
Rostock, Germany, (16) Department of
Chemistry, University of Alabama at
Birmington, Birmingham, Alabama, United
States, (17) Physical and Theoretical
Chemistry, Elsevier, Amsterdam, The
Netherlands
(GDC) software and compared against the
NIST Data Archive using the dynamic-dataevaluation algorithms of the NIST
ThermoData Engine (TDE) software. A Data
Report is generated and typographical or
data-consistency problems are resolved
before acceptance. These procedures are
mandatory. A review of successes and
challenges will be described, together with
new online support tools.
9:45 - Intermission
10:00 - 40 - Reproducibility in
cheminformatics and computational
chemistry research: Certainly we can do
better than this
Gregory A. Landrum,
[email protected], Novartis
Institutes for BioMedical Research, Basel,
Switzerland
Reproducibility is a central principle in
scientific research. According to the American
Chemical Society's “Ethical Guidelines to
Publication of Chemical Research”: An
author's central obligation is to present an
accurate and complete account of the
research performed, absolutely avoiding
deception, including the data collected or
used, as well as an objective discussion of the
significance of the research. Data are defined
as information collected or used in generating
research conclusions. The research report and
the data collected should contain sufficient
detail and reference to public sources of
information to permit a trained professional
to reproduce the experimental observations
[1]. This presentation will explore some of the
implications of this for the publication of new
computational methods and do a survey of
the current state of affairs in the
cheminformatics/computational chemistry
literature. We will close with some
suggestions, drawn from scientific journals in
other areas, about how we can do better.
In 2008, the Journal of Chemical and
Engineering Data, Fluid Phase Equilibria, The
Journal of Chemical Thermodynamics,
International Journal of Thermophysics, and
Thermochimica Acta agreed to implement a
new process for submission of manuscripts
that include experimental thermodynamic
and transport property data. For articles
reporting new property data, NIST provides
an initial report of relevant data sources from
the NIST Archive (a Literature Report). This
report is provided to Editors, who at their
discretion, forward it to reviewers and/or
authors. After peer review, but before
acceptance, the experimental data are
captured at NIST with Guided Data Capture
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Chemical Information Bulletin Vol. 65(1) Spring 2013
[1]
http://pubs.acs.org/userimages/ContentEdito
r/
1218054468605/ethics.pdf
2004) Bioconductor Project Working Papers.
Working Paper
2.http://biostats.bepress.com/bioconductor/
paper2. 2. R Development Core Team (2012).
R: A language and environment for statistical
computing. R Foundation for Statistical
Computing, Vienna, Austria. ISBN 3-90005107-0, URL http://www.R-project.org/. 3.
http://yihui.name/knitr/ 4.
http://daringfireball.net/projects/markdown/
5.
https://bitbucket.org/rivanvx/beamer/wiki/H
ome
10:30 - 41 - Reproducible research applied to
cheminformatics experiments
Paul J Kowalczyk,
[email protected], Department of
Computational Chemistry, SCYNEXIS, Research
Triangle Park, NC 27709-2878, United States
Gentleman and Temple Lang1 define
reproducible research as “¼research papers
with accompanying software tools that allow
the reader to directly reproduce the results
and employ the methods that are presented
in the research paper.” We demonstrate how
one might report cheminformatics
experiments as instances of reproducible
research, i.e.,how one might author and
distribute integrated dynamic documents that
contain the text, code, data and any auxiliary
content needed to recreate the
computational results. We show how the
contents of these documents, including
figures and tables, can be recalculated each
time the document is generated. Opensource tools are used for all document
generation: the R software environment2 is
used to process chemical structures and mine
and analyze biological and chemical data; the
knitr3 package is used to generate reports
(PDF); the markdown4 package is used to
generate valid (X)HTML content; and the
beamer5 package is used to create slides for
presentation. Specific examples are
presented for the visualization, analysis and
mining of publicly available antimalarial
datasets, with particular attention paid to
automatically generating PDF reports, slides
for presentations and valid (X)HTML content.
All text, code, data and auxiliary content will
be made freely available. 1 Gentleman,
Robert &Duncan Temple Lang, “Statistical
Analyses and Reproducible Research” (May
11:00 - 42 - Mythbusting scientific
knowledge transfer with nanoHUB.org:
Collaborative research and dissemination
with quantifiable impact on research and
education
Gerhard Klimeck, [email protected],
Network for Computational Nanotechnology,
Purdue University, West Lafayette, IN 47907,
United States
Gordon Moore's 1965 prediction of continued
semiconductor device down-scaling and
circuit up-scaling has become a self-fulfilling
prophesy. Open source code development
and sharing of the process modeling software
SUPREM and the circuit modeling software
SPICE ultimately transitioned into all
electronic design software packages that
power today's 280 billion dollar
semiconductor industry. Can we duplicate
such multi-disciplinary software, leading to
true economic impact? What technologies
might advance such a process? How can we
deliver such software to a broad audience?
How can we teach the next-generation
engineers and scientists on the latest
research software? This presentation will
show how nanoHUB.org addresses these
questions. By serving a community of 240,000
users in the past 12 months with an evergrowing collection of 3,100 resources,
including over 260 simulation tools,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
nanoHUB.org has established itself as “the
world's largest nanotechnology user facility”
[1]. [1] Quote by Mikhail Roco, Senior Advisor
for Nanotechnology, National Science
Foundation.
are the “values” associated with a variable
describing taste? Such variables, called
linguistic variables, take on values such as
sweet, sour, and bitter, which can be
represented by fuzzy sets. The talk will
explore how these novel variables are defined
and how they can be applied in food
informatics and related fields.
Monday, April 8, 2013
FoodInformatics: Applications of Chemical
Information to Food Chemistry - PM Session
Morial Convention Center
Room: 349
Cosponsored by AGFD
2:00 - 44 - Exploring the chemical space of
flavors and fragrances with the chemical
universe database
Jean-Louis Reymond1, [email protected], Lars Ruddigkeit1,
Mahendra Awale1, Guillaume Godin2. (1)
Department of Chemistry and Biochemistry,
University of Berne, Berne, Switzerland, (2)
rue des Jeunes 1, Firmenich SA, Geneva,
Switzerland
Jose Medina-Franco, Karina Martinez
Mayorga, Organizers
Jose Medina-Franco, Presiding
1:30 pm - 5:30 pm
1:30 - Introductory Remarks
The chemical space describes the ensemble of
all organic molecules. Recently we reported
the Chemical Universe Database GDB-13
enumerating 977 million molecules of up to
13 atoms of C, N, O, S and Cl. Herein we
report the analysis and visualization of
analogs of typical flavors and fragrance
compounds found in the database. Analog
searching was performed using a searchable
version of GDB-13 based on MQN-similarity.
The analysis illuminates a vast yet well
defined chemical space that offers many
opportunities to broaden the range of flavors
and fragrances to new structural types.
1:35 - 43 - Soft and fuzzy approach to food
informatics
Gerald M Maggiora,
[email protected], Pharmacology
&Toxicology/Bio5 Institute, University of
Arizona, Tucson, AZ 85721, United States and
Cancer &Cell Biology Division, Translational
Genomics Research Institute, Phoenix, AZ
85004, United States
Since its inception at the beginning of the
computer age, chemical informatics has
played a growing role in many facets of
chemical research. Most of its applications
are in pharmaceutical research, but it is
beginning to have an impact in other fields
such as materials and food science. In
chemical informatics, molecules are
represented by descriptors associated with
their structural features or properties, which
typically are specified in terms of numerical or
categorical variables. Some descriptors,
however, cannot be described by such
variables because of their inherent
uncertainty or vagueness. For example, what
2:25 - 45 - Tracing pharmacophore
determinants of natural- and nutritional-like
components in epigenetics and metabolism
Alberto Del Rio, [email protected],
Department of Experimental, Diagnostic and
Specialty Medicine (DIMES), University of
Bologna, Bologna, Bologna 40126, Italy
The pharmacology of natural and
nutraceutical components is crucial in many
cellular processes. Several clinical,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
physiopathological and epidemiological
studies highlight the detrimental or beneficial
role of natural/nutritional factors in
conjunction with epigenetic and metabolic
alterations. Furthermore there is growing
evidence that metabolism is linked to
epigenetic changes, especially in cancer
pathologies. Examples of natural/nutritional
molecules are: insulin, flavanol-rich
compounds, short-chain fatty acids, indoles,
and other dietary components that can be
converted by cell metabolism into chemical
intermediates implicated in epigenetic
alterations. A deeper understanding on how
metabolism and epigenetic are influenced by
these components requires a molecular-level
knowledge encompassing several aspects like
the polypharmacological role of these
compounds. In this context, pharmacophorebased techniques are described as a valuable
chemoinformatic tool for tracking-down
molecular determinants of nutriepigenomics
and nutrimetabolomics molecular
mechanisms.
molecule(s) from an organism is(are)
responsible for the biological activity and the
biological pathway(s) involved. An exciting
outcome of this approach is that it not only
provides evidence of the biological properties
of plants but can also be applied to
compounds from other sources. Thus, reverse
pharmacognosy allows to accelerate the R&D
of active molecules and ingredients.
3:15 - 47 - Flavor network: Exploring the
principles of food pairing
Sebastian E Ahnert1, [email protected],
Yong-Yeol Ahn2, Albert-Laszlo Barabasi3. (1)
Department of Physics, University of
Cambridge, Cambridge, United Kingdom, (2)
School of Informatics and Computing,
University of Indiana, Bloomington, IN 47408,
United States, (3) Department of Physics,
Northeastern University, Boston, MA, United
States
The cultural diversity of culinary practice, as
illustrated by the variety of regional cuisines,
raises the question of whether there are any
general patterns that determine the
ingredient combinations used in food today
or principles that transcend individual tastes
and recipes. We introduce a flavor network
that captures the flavor compounds shared by
culinary ingredients. Western cuisines show a
tendency to use ingredient pairs that share
many flavor compounds, supporting the socalled food pairing hypothesis. By contrast,
East Asian cuisines tend to avoid compound
sharing ingredients. Given the increasing
availability of information on food
preparation, our data-driven investigation
opens new avenues towards a systematic
understanding of culinary practice. In light of
this we also discuss a variety of datasets on
food ingredients and flavour compounds and
how to combine them using large-scale data
analysis.
2:50 - 46 - Reverse pharmacognosy: From
molecules to active ingredients
Quoc Tuan Do,
[email protected], Sylvain
Blondeau, Philippe Bernard.
Chemoinformatics, Greenpharma S.A.S.,
Orleans, Loiret 45100, France
A huge amount of data has been generated
by decades of pharmacognosy supported by
the rapid evolution of chemical, biological and
computational techniques. How can we cope
with this overwhelming mass of information?
Reverse pharmacognosy was introduced with
this aim in view. It proceeds from natural
molecules to organisms that contain them via
biological assays in order to identify an
activity. In silico techniques and particularly
inverse screening are key technologies to
achieve this goal efficiently. Reverse
pharmacognosy allows us to identify which
3:40 - Intermission
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Chemical Information Bulletin Vol. 65(1) Spring 2013
3:50 - 48 - USP reference standards as valueadded information sources in the Food
Chemicals Codex (FCC)
Christina L. Cole, [email protected], Department of
Foods, Dietary Supplements, and Herbal
Medicines, United States Pharmacopeial
Convention, Rockville, MD 20852, United
States
safety. This literature includes discussion on
the chemistry of the major and minor food
components, food additives, contaminants,
and their corresponding metabolism and
toxicology. This presentation will detail how
the Reaxys database supports the search and
retrieval of information pertinent to food
chemistry. This includes reaction and
substance / chemical property information. In
order to ensure we cover relevant journals,
and the appropriate data from within those
journals, we have implemented an updated
excerption strategy. We will discuss the
identification, and excerption of relevant data
from the appropriate literature with
particular reference to the food chemistry
literature.
The FCC is a compendium of internationally
recognized standards for the purity and
identity of food ingredients, featuring ~1100
monographs for food-grade chemicals,
processing aids, foods, flavoring agents,
vitamins, and functional food ingredients.
With public and stakeholder guidance, FCC
establishes vetted food ingredient
specifications and supporting test procedures
that help manufacturers, suppliers, and
regulators safeguard the food supply; USP
Reference Standards are often incorporated
into these monograph methods. The use of
USP Reference Standards facilitates rapid and
unbiased decisions on the quality and identity
of food ingredients; enhances the reliability of
analytical test results; and serves as a valueadded information source wihtin the context
of associated FCC monographs. This talk will
focus on this "extra" information contained
by the Reference Standard, and how it
complements other FCC and USP activities
such as the Food Fraud Database and recent
workshops on the identity and
characterization of functional food
ingredients and probiotics.
4:40 - 50 - Profiling the trace metal
composition of wine as a function of storage
temperature and packaging type
Helene Hopfer1,2, [email protected],
Jenny Nelson3, Carolyn L Doyle1,2, Hildegarde
Heymann1, Alyson E. Mitchell2,4, Susan E.
Ebeler1,2. (1) Viticulture and Enology,
University of California, Davis, CA 95616,
United States, (2) Food Safety and
Measurement Facility, University of California,
Davis, CA 95616, United States, (3), Agilent
Technologies Inc., Santa Clara, CA 95051,
United States, (4) Food Science and
Technology, University of California, Davis, CA
95616, United States
Trace metal patterns in grapes and wines are
mostly studied to determine the geographical
origin and authenticity using highly sensitive
instrumentation such as inductively coupled
plasma mass spectrometry (ICP-MS).
However, ICP-MS can also be used to study
possible metal contamination of wines during
the winemaking and storage processes. In the
present study we looked at the changes in the
trace metal composition of Cabernet
Sauvignon wine that had been stored in
different packaging configurations (various
4:15 - 49 - Reaxys as an information resource
for food chemistry
David Evans1, [email protected],
Juergen Swienty-Busch2. (1) Reed Elsevier
Properties SA, Neuchâtel, Switzerland, (2)
Elsevier Information Systems GmbH,
Frankfurt, Germany
There is a wide and varied literature related
to food sciences, including chemistry and
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Chemical Information Bulletin Vol. 65(1) Spring 2013
closures and glass alternatives) for a period of
6 months. The effect of storage temperature
and packaging type was studied by
monitoring 15 elements using a quantitative
ICP-MS method. Significant changes in the
elements Cr, V, Sn and Pb were found among
the different packaging types and the storage
temperatures. Multivariate statistical analysis
tools were used to evaluate the changing
metal profiles in the wines with the various
packaging treatments.
Monday, April 8, 2013
Scholarly Communication: New Models, New
Media, New Metrics - PM Session
Morial Convention Center
Room: 352
Cosponsored by YCC
William Town, Colin Batchelor, David
Martinsen, Organizers
Colin Batchelor, William Town, Presiding
1:00 pm - 5:30 pm
5:05 - 51 - Mining the protein space to
determine prevalence of fragments identical
with allergenic epitopes - chicken egg
protein fragments as an example
Piotr Minkiewicz, [email protected],
Monika Protasiewicz, Małgorzata Darewicz,
Karolina Hurman, Anna Iwaniak. Department
of Food Biochemistry, University of Warmia
and Mazury in Olsztyn, Olsztyn, Poland
1:00 - Introductory Remarks
1:05 - 52 - Supplementary journal article
materials: Summary of the NISO/NFAIS
recommendations
David P Martinsen, [email protected],
Publications DIvision, American Chemical
Society, Washington, DC 20036, United States
As journals migrated from print to the Web,
the nature of supplemental materials began
to change. In the print world, supplemental
materials were usually text or graphics which
were too expensive to be formated and
printed, and so were distributed on
microfiche. Datasets were also included as
printouts of tables of numbers. The digital
world brought the promise of overcoming the
limitations of print to more easily publish and
distribute supplemental materials in a more
usable form. The result has been a wide
degree of variation among publishers, varying
expectations among authors, editors,
reviewers and readers, and an increasing
volume of supplemental materials which
places an increasing burden on all parts of the
publication process. NISO and NFAIS
convened a working group to examine the
current status of supplemental journal article
materials and to recommend best practices
for publishing these materials. A summary of
the recommendations will be presented.
The aim of this study was to find proteins
containing fragments identical with epitopes
experimentally detected in allergenic chicken
egg proteins. Epitope sequences were taken
from BIOPEP database. WU-BLAST program
was used for the UniProt protein sequence
database screening. Both short fragments
containing 5-8 amino acid residues and longer
ones containing at least 9 residues were
present in protein sequences. Longer ones
were present only in the homologs of the
chicken egg proteins. The shorter fragmens
were found also in other proteins. The
existence of common epitopes in proteins of
different species, may lead to occurrence of
cross-reactivity. The presence of such
fragments indicates at least the existence of
individuals whose antibodies interact with set
of proteins containing the same epitopes. The
approach involving protein database
screening may be useful in searching the new
allergenic proteins including epitopes
common to known allergens.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
1:35 - 53 - Digital research that is
discoverable, citable, and linked to primary
research literature: The Data Citation Index
Daphne Grecchi,
[email protected],
Scientific &Scholarly Research, Thomson
Reuters, Philadelphia, PA 19130, United
States
with rapid technological advances, a
paradigm shift toward the digital world is
occurring. Mobile devices add another
dimension in the shift, making the digital
world readily accessible from anywhere. For
scientists, this shift has already resulted in the
transition from physical libraries and paper
journals to websites and electronic tools to
conduct scholarly research and to
communicate with colleagues and
collaborators. While each person has his/her
own research workflow, the components that
make up this process are similar. We present
here a complete integrated research
management and collaboration suite, which
features a reference management system,
calendars, and task management for
effectively organizing research work. This is
combined with an online social profile and
many other features to facilitate the complex
and entropic sharing process.
The worldwide growth in data repositories
and the requirement by funding agencies and
publishers to have researchers put their data
in them have increased the need for a
comprehensive view of research data and its
use. Digital scholarly data plays an important
role in research, advancing important
scientific discoveries through validated data
points. Data Citation Index, available on
Thomson Reuters Web of Knowledge focuses
on the deployment of a citation resource that
makes research data discoverable, citable and
seamlessly linked to the primary research
literature. Now quality research data from
data repositories across disciplines and
around the world can be searched and
assessed from within a single point of access,
where data can be viewed within the context
of the scholarly research it supports. This
presentation reviews how the Data Citation
Index connects digital research to powerful
new discovery tools and how the inclusion of
data and digital scholarship maximizes the
benefits of powerful citation search
capabilities and navigation features available
within Web of Knowledge.
2:35 - Intermission
2:50 - 55 - Evolving with our community: The
RSC's approach to the challenges and
opportunities of scientific communication
Richard Kidd, [email protected], James Milne.
Royal Society of Chemistry, Cambridge, United
Kingdom
2:05 - 54 - From inception to collaboration to
publication: A complete integrated research
management platform for researchers
Judy Chen, [email protected], Editorial Office
Operations, American Chemical Society,
Washington, District of Columbia 20036,
United States
We will be reporting on the RSC's approach to
evolving business models, including the
support to UK institutions and researchers to
help prepare for the transition to OA resulting
from the recent Finch recommendations and
RCUK policy. We will also report on the
expansion of the publishing portfolio, and on
how we are developing the RSC's support for
primary data. The RSC's aim is to test and
evolve new technological, social and business
models in parallel to provide support for the
research community.
As a result of the vast amount of information
and resources available on the web coupled
3:20 - 56 - We're not in Kansas anymore
Roger Schenck, [email protected],
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Marketing, Chemical Abstracts Service,
Columbus, Ohio 43202, United States
experiences in engaging the community to
interact with our various forms of content
and discuss new approaches we are utilizing
to encourage crowdsourced participation.
As the only organization in the world whose
objective is to find, collect, and organize all
publicly disclosed substance information, CAS
is challenged to keep pace with rapidly
changing publication models in the scientific
community. This presentation will cover ways
in which CAS is handling the growing number
of ahead-of-print articles, web-only
publications, open access journals, the
synthetic information and experimental data
increasingly reported in supplementary
material, and even the new visual journals
where articles are actually videos of
experiments. The talk will conclude with
examples of how CAS is working with primary
publishers and patent authorities to deliver
chemistry research to the scientific
community in a more integrated model.
4:20 - Intermission
4:30 - 58 - Science comedian's guide to
communicating science to general audiences
Brian Malow,
[email protected], North
Carolina Museum of Natural Sciences,
Raleigh, NC 27601, United States
This presentation will provide an overview of
the lessons learned in communicating science
for over 15 years to both general audiences
and specialized groups (including NASA, NIST
and the ACS). Currently working on science
communications at the North Carolina
Museum of Natural Sciences, Brian Malow
has made a number of science videos for
Time Magazine's website and contributed a
number of audio essays to Neil deGrasse
Tyson's radio show. He is Earth's selfproclaimed premier science comedian and
this presentation is sure to both amuse and
educate.
3:50 - 57 - Challenging, cajoling, and
rewarding the community for their
contributions to online chemistry
Antony J Williams1, [email protected],
Valery Tkachenko1, Alexey Pshenichnov1, Will
Russell2, Jack Rumble2, David Leeming2. (1)
Cheminformatics, Royal Society of Chemistry,
Wake Forest, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom
Monday, April 8, 2013
Food for Thought: Alternative Careers in
Chemistry - PM Session
Morial Convention Center
Room: 350
Cosponsored by PROF, YCC
Chemistry online is represented in various
ways including publications, presentations,
blog posts, wiki-contributions, data
depositions, curations and annotations.
Encouraging participation from the
community to participate in and comment on
the information delivered via these various
formats would likely provide for a rich dialog
exchange in some cases and improved data
quality in others. At the Royal Society of
Chemistry we have a number of platforms
that are amenable to contribution. This
presentation will provide an overview of our
Donna Wrublewski, Patricia Meindl,
Organizers
Patricia Meindl, Presiding
1:15 pm - 5:15 pm
1:15 - Introductory Remarks
1:20 - 59 - From studying block copolymers
to chemical information: A journey of an
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Chemical Information Bulletin Vol. 65(1) Spring 2013
alternative chemistry career as an academic
science librarian
Vincent F Scalfani, [email protected],
University Libraries, The University of
Alabama, Tuscaloosa, AL 35487, United States
2:20 - 61 - Cheminformatics career at the
Royal Society of Chemistry, UK
Colin Batchelor, [email protected], Royal
Society of Chemistry, United Kingdom
I am a Senior Cheminformatics Analyst at the
Royal Society of Chemistry in Cambridge, UK,
working on text-mining, semantic web
technology and ChemSpider. My doctoral
work, however, was on applying multichannel
quantum defect theory to the ionization
dynamics of small molecules in the gas phase.
In this talk I will discuss what this entails in
practice, how my background in theoretical
chemistry and journal publishing prepared me
for it and what it's like to work in
cheminformatics for a learned society.
Unbeknownst to many chemistry graduate
students, crucial skills relevant to a career in
science informatics, information technology
and librarianship are acquired daily while
working on their dissertations - both in and
outside of the laboratory. For example,
planning synthetic routes, analyzing data
trends, and writing technical papers all
require information seeking skills. This
presentation will highlight how to transition
from the laboratory to the library, as well as
how Chemists can bring a fresh perspective to
the Library. My personal journey of
transitioning from studying block copolymer
nanomaterials as a Ph.D. Chemistry student
to working as the new Science Librarian at the
University of Alabama will be used as one
example of how to make this transition. In
addition, projects started in my first year at
the University of Alabama Rodgers Science
and Engineering Library will be discussed.
2:50 - 62 - Patent law as a non-traditional
career in chemistry
Sarah P Hasford,
[email protected],
McGuireWoods, LLP, Tysons Corner, VA
22102, United States
This presentation will focus on a patent
attorney's role in protecting innovation and
discuss the ups and downs of practicing
patent law for those who may be interested
in exploring a patent law career for
themselves.
1:50 - 60 - Successful careers in science: Why
moving away from the bench brings you
closer to advancing research
Lily Khidr, [email protected], Elsevier, New
York City, New York 10010, United States
3:20 - Intermission
This lecture will delineate why it is
advantageous for active research scientists to
consider the road to becoming an Editor and
Publisher, what the competitive process of
achieving these high-profile positions entails,
and the value-add of the job within an
evolving scientific and academic landscape.
Dr. Khidr is an academic research scientist
that has served as an Editor at both Nature
and Science Magazines, and currently holds
the position of Publisher at Elsevier in New
York City.
3:35 - 63 - Role of personal interests,
motivation, and timing in the transitioning to
a new career
Svetla Baykoucheva, [email protected],
White Memorial Chemistry Library, University
of Maryland, College Park, MD 20742, United
States
This paper shows how someone with an
educational and research background in
chemistry and the life sciences (BS and MS in
Chemistry, PhD in Microbiology) could
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Chemical Information Bulletin Vol. 65(1) Spring 2013
maintain for many years parallel interests in
citation indexing that led to a seamless
transition to a new career in information
science and librarianship. From working at the
lab bench and publishing in scientific journals,
to joining a scientific publisher (ACS) as a
librarian, and finally, to going back to
academic life (University of Maryland, College
Park) to manage a chemistry library and teach
chemical information were career turns that
required strong motivation and depended to
a large degree on timing.
branch experience will be discussed. The talk
will include a discussion of how fellowships
translated into careers in government and a
discussion of how applicants can prepare
competitive applications.
5:05 - Concluding Remarks
Monday, April 8, 2013
Sci-Mix - EVE Session
Morial Convention Center
Room: Hall D
4:05 - 64 - From the bench to the board
Rebecca Boudreaux,
[email protected], Oberon Fuels, La
Jolla, CA 92038, United States
Jeremy Garritano, Organizers
8:00 pm - 10:00 pm
1 - Characterizing the diversity and biological
relevance of the MLPCN assay manifold and
screening set
Jun Huan, [email protected], EECS, Univ. of
Kansas, lawrence, ks 66049, United States
What does it take to go from chemist to
company co-founder? How can you develop
from scientist to startup expert?
This talk will discuss transitioning from the
bench to the board, and draw on my
background in chemistry, business, and
leadership. As a PhD-trained chemist, I?ve
used my scientific expertise to launch
ventures designed to treat cancer and
develop a cleaner alternative to diesel, among
others. I will show how my educational
background played a key role in helping me
develop the skills necessary to pursue these
opportunities, and offer advice for those
interested in a similar career.
The NIH Molecular Libraries Probe Production
Centers Network (MLPCN) aims to remediate
key deficiencies in drug discovery and
chemical biology, through pursuit of
therapeutically feasible but unprofitable drug
targets, undruggable genes of biochemical
interest, and development of chemically
diverse, biologically relevant screening sets.
This paper evaluates the novelty of MLPCN
targets, their propensity for undergoing
modulations of biochemical or therapeutic
relevance, the degree of chemical diversity
inherent in the MLPCN screening set, and
biogenic bias of the set. Our analyses suggest
that MLPCN targets cover biologically
interesting pathway space that is distinct
from established drug targets, but may
include genes whose overly complex protein
interactions may obfuscate pathway effects
and enable therapeutically undesirable sideeffect risks. We find the MLPCN screening set
to be chemically diverse, and it has greater
biogenic bias than comparable collections of
4:35 - 65 - Political "science": Opportunities
for chemists in science policy
Ticora V Jones, [email protected], Office of
Science &Technology, US Agency for
International Development, Washington, DC,
United States
This talk will describe the opportunities for
chemists to involve themselves in the arena
of science policy making as an alternative
career. The experience of a past science
policy fellow with Legislative and Executive
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Chemical Information Bulletin Vol. 65(1) Spring 2013
commercially available compounds. Biogenic
enhancements such as incorporation of more
metabolite-like chemotypes are suggested.
University of New York, New York, NY, United
States, (2) Graduate Center, City University of
New York, New York, NY, United States
4 - PubChem widgets
Lianyi Han, [email protected], National
Center for Biotechnology Information,
National Institutes of Health, Bethesda, MD
20894, United States
Recent high-throughput screens have
generated a lot of protein-ligand interaction
data; for example, over one million
compounds are associated with the 4422
proteins in ChEMBL. Recent attempts to mine
and visualize this large protein-ligand
interaction dataset have mapped chemicals
into a high-dimensional feature space and
visualized it using dimensionality reduction
techniques. We propose a different approach
to exploring the protein-ligand interactome
efficiently, effectively, and intuitively. We link
all chemicals and targets into an all-against-all
chemical similarity network and target
similarity network, respectively. The networks
are connected as a bipartite graph through
protein-ligand interactions. Efficient graph
clustering and mining algorithms are applied
to identify chemical and protein patterns
underlying binding promiscuity and
specificity. Although the chemical/protein
similarity network is computationally
intensive, it need only be built once and
updated regularly. As demonstrated in case
studies for anti-infectious drug discovery, our
method may facilitate drug repurposing, sideeffect prediction, and polypharmacology drug
design.
Modern interactive web and mobile
applications for chemistry and biology often
need to integrate information from multiple
resources, such as biochemical analysis,
patents, and publications. This typically
requires an underlying data warehouse
containing billions of chemical and bioactivity
records coupled with web services that
deliver "Asynchronous JavaScript and XML"
(AJAX) and JSONP(or "JSON with padding")
content to applications. PubChem Widgets
provide a rapid development tool to create
content-rich and interactive UIs without
requiring the development of such a data
warehouse. These widgets show commonly
requested PubChem data views, such as 1)
patents associated with a PubChem
compound or substance; 2) bioactivity
outcomes for a PubChem compound,
substance, or bioassay; 3) Literature available
for a compound, substance, or bioassay.
These widgets are easily embedded into your
own web application or HTML pages, and can
also be used to access annotation data from
native desktop and mobile applications. Beta
release available:
http://pubchem.ncbi.nlm.nih.gov/widget/doc
s/widget_help.html.
6 WITHDRAWN
17 - Encoded Library Technology data
analysis: Finding the grain of sand you want
without getting a sunburn
Kenneth E Lind, [email protected], Neil
R Carlson, Ninad V Prabhu, Jeff A Messer.
MDR Boston, GlaxoSmithKline, Waltham, MA
02451, United States
16 - On-line graph mining and visualization
of protein-ligand interactome
Clara Ng1, [email protected], Lei
Xie1,2, [email protected]. (1)
Department of Computer Science, City
Encoded Library Technology (ELT) is a part of
GSK's integrated Hit ID strategy. ELT involves
creation of large combinatorial libraries
whose members (sometimes over a billion!)
are encoded by a unique combination of DNA
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Chemical Information Bulletin Vol. 65(1) Spring 2013
tags. Binders to a molecular target are
selected from these libraries and identified
using next-generation DNA sequencing. We
have developed a platform for translating
sequence data back to the encoded chemical
warhead, detecting features that are enriched
in the selection, and summarizing and
annotating the selection experiment. Each
week our platform processes over 100 million
DNA sequences - larger than the entire
human genome. Data visualization is
integrated into the TIBCO Spotfire platform,
allowing scientists to view summaries of the
large data sets, determine the most
important chemical space, and then drill
down to specific results to prioritize
compounds for synthesis and assays. We will
describe method details and present
examples to highlight our analysis and
visualization tools.
26 - iBIOMES: Managing and sharing large
biomolecular simulation datasets in a
distributed environment with iRODS
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3. (1)
Department of Biomedical Informatics,
University of Utah, Salt Lake City, Utah 84112,
United States, (2) Department of Medicinal
Chemistry, University of Utah, Salt Lake City,
Utah 84112, United States, (3) Center for
High-Performance Computing, University of
Utah, Salt Lake City, Utah 84112, United
States
During this presentation we will introduce the
architecture of iBIOMES (Integrated
BIOMolEcular Simulations), a distributed
system for biomolecular simulation data
management allowing storage and indexing
of large datasets generated by Molecular
Dynamics (MD) simulations, along with ab
initio calculation results. The system
architecture is based on iRODS, a data
handling system developed by RENCI, and
influenced by the experience gained from the
Storage Resource Broker (SRB) system. iRODS
provides the tools to register, move, and
lookup files that are distributed over the
network and stored in different types of disk
(e.g. HPC servers, files servers, archive tapes).
Registered files can be queried and retrieved
based on system or user-defined metadata.
We created customized interfaces on top of
iRODS to facilitate the data registration
process for biomolecular simulation datasets
(e.g. AMBER, Gaussian). The process is highly
customizable through XML descriptors,
enabling users to choose which piece of data
should be displayed to summarize the
registered experiments. Data registration
does not require physical transfer of the data,
which makes it a great solution for
researchers who want to expose existing
datasets. Input and output files can be made
available for download within a collaborative
network to allow replication of results or
19 - How to highlight hits: Advances in visual
data analytics tools for HTS data
Jesse A. Gordon,
[email protected], Jess Sager.
Application Science, Dotmatics, Ltd., Woburn,
MA 01801, United States
We face a huge dataset from a screening run
and we want to analyze the results to pick
compounds for the next screening run. How
do we sift through the millions of data points
to figure out which are meaningful hits, and
then organize those hits into a database from
which we can intelligently predict good
prospects for the next screening run? We face
a series of challenges in HTS data analysis
which will be outlined in this presentation
followed by solutions offered through
modern chemoinformatics and visual data
analytics tools. We look at the difference
between the "Old Way" -- grid after grid in
Excel with manual calculations -- and the
"New Way" -- clicking on visually distinctive
points highlighted in red on automaticallygenerated curves.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
comparison between methods (e.g. different
force-fields). Finally data summarization and
management are facilitated through a rich
web interface that offers different
visualization components for 3D structures
and analysis data (e.g. time series plots,
heatmaps). iBIOMES represents one of the
first efforts to create an infrastructure for
researchers to manage their MD data locally,
expose their data to the community, and
create collaborative networks.
learning methods to predict properties of
various chemical properties, showing the
importance of statistical and visual validation
of found patterns.
29 - Discovery of TLR2 antagonists by virtual
screening
Manuela S Murgueitio1, [email protected], Sandra Santos-Sierra2, Gerhard
Wolber1. (1) Institute of Pharmacy,
Pharmaceutical Chemistry, Freie Universität
Berlin, Berlin, Berlin 14195, Germany, (2)
Institute of Clinical Pharmacology,
Medizinische Universität Innsbruck, Innsbruck,
Tirol A-6020, Austria
28 - New cheminformatics microscopes:
Combining semantic web technologies,
cheminformatical representations, and
chemometrics for understanding and
predicting chemical and biological properties
Egon L Willighagen,
[email protected],
Department of Bioinformatics - BiGCaT,
Maastricht University, Maastricht, The
Netherlands
Toll-like receptors (TLRs) represent the first
barrier in innate immune response and act as
key players in the development of chronic
inflammatory and autoimmune diseases.
Thus, interest for identifying small organic
molecules modulating TLRs has risen. In this
study we present a virtual screening approach
for the identification of novel TLR2
antagonists, combining ligand- and structurebased design. First, we performed a shapeand feature-based similarity search against
commercially available compound collections,
using TLR2 agonists from literature and two
TLR2 antagonists previously identified inhouse as query structures. Second, molecular
interaction fields (MIFs) of the TLR2 binding
site were calculated to derive a structurebased 3D pharmacophore that was then used
for virtual screening. A selection of virtual
screening hits was biologically tested in a cellbased assay for TLR2 inhibition, leading to
several compounds with antagonistic activity
(IC50) in the micromolar range.
Cheminformatics is a computational
microscopy with which we study chemical
properties. My research develops new
microscopes based on cheminformatics, using
semantic web and chemometrics
technologies. This resulted in and contributed
to many computational methods to handle
chemical structures and predict their
chemical, physical, and biological properties.
These methods include computational
software like the Chemistry Development Kit,
visualization tools like Jmol, JChemPaint, and
Bioclipse, and information retrieval
technologies like OSCAR4, as well as data
exchange standards like the Chemical Markup
Language, the CHEMINF ontology, and other
semantic solution aimed at reducing
information loss, and new public chemical
knowledge based, such as the Blue Obelisk
Data Repository and the NanoWiki with
toxicological properties of nanomaterials.
These and other tools have used in the
combination with statistical and machine
31 - On the compound annotation and
cleaning the GSK screening collection
initiative: The utility of an Inhibition
Frequency Index (IFI)
Subhas J Chakravorty,
[email protected], James A
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Chan, Juan Luengo, Nicole M Greenwood,
Ioana Popa-Burke, Ricardo Macarron. CSC,
Sample Technologies, GSK, Upper Providence,
PA 19426, United States
linear process, with sequential optimization
of compound parameters and hand-offs
between teams, starting with a very basic
analysis of primary screening data. Often the
“best” series as identified by early assays are
not the “best” series for late optimization.
This talk will ask how we can improve lead
series and potentially identify drug candidates
by improved analysis early in the lead ID
process. We will look at the value of and
methods for analyzing multiple assays in
parallel. An example of parallel optimization
will be discussed where a phenotypic assay
and a targeted assay were run in parallel.
Data will be shown that supports the
conclusion that running the parallel assays
directs the team into different chemical space
than a more traditional sequential approach.
In addition, a novel method for analyzing the
success of series expansion will be presented
in this context.
High throughput screening (HTS) constitutes a
critical tool for the identification of lead
molecules from primary screening assays for
novel targets. GlaxoSmithKline (GSK) has
continuously invested in the development
and curation of its HTS collection to maximize
the number of quality starting points for drug
discovery and reduce the number of false
positives from primary screens. An Inhibition
Frequency Index (IFI) has been defined as a
measure of promiscuity of individual
compounds in HTS primary assays based upon
activities tabulated over time in GSK's
exhaustive screening assay tables. In this talk,
we will present our analysis of the IFI profile
across the GSK HTS collection. We will
characterize the IFI profile with respect to
desired physical properties, will discuss
obvious substructures that may be less
attractive as starting points, and will describe
new classes of nuisance compounds revealed
by our IFI analysis. In addition, we will
examine the IFI of promiscuity filters
described in the literature. There are many
reasons why any particular molecule might
display promiscuity: physical properties of the
compound, properties of the target or target
class, details of the assay and the assay
technology and methodology. All of these
factors must be considered when deciding
whether to remove or retain a compound in a
curated HTS collection.
33 WITHDRAWN
36 - From hits to leads: Data visualization of
chemical scaffolds beyond traditional SAR
exploration
Tyler Peryea, [email protected], John
Braisted, Ajit Jadhav, Rajarshi Guha, Noel
Southall, Dac-Trung Nguyen. National Center
for Advancing Translational Sciences, Division
of Preclinical Innovation, Rockville, Maryland
20850, United States
Turning hits from an HTS campaign into
potential leads is a critical part of early stage
therapeutic discovery. Often, this amounts to
distilling thousands of HTS hits into a small
number of manageable candidate series (or
singletons in some cases) for lead
optimization. While the process is fairly
straightforward, the tools involved can range
anywhere from ad-hoc scripts to custom built
solutions. We will describe methods that take
a set of suitable seed compounds (e.g., the
result of activity selection), extract a set of
32 - Analyzing screening and similarity
searching outcome in light of multiple
approaches to the same target
Tina Garyantes, [email protected],
MAXSAR Biopharma, Warren, NJ 07059,
United States
Traditional candidate discovery tends to be a
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Chemical Information Bulletin Vol. 65(1) Spring 2013
relevant scaffolds, and place the scaffolds in
the context of high-quality external data
sources. We couple the scaffold driven
analytics with visualizations of scaffold
structural properties and associated activities
that allow efficient and intuitive exploration
of candidate series. We will finally describe a
software tool that implements these methods
and highlight its utility on HTS data from the
Molecular Libraries Program.
automatically generating PDF reports, slides
for presentations and valid (X)HTML content.
All text, code, data and auxiliary content will
be made freely available. 1 Gentleman,
Robert &Duncan Temple Lang, “Statistical
Analyses and Reproducible Research” (May
2004) Bioconductor Project Working Papers.
Working Paper
2.http://biostats.bepress.com/bioconductor/
paper2. 2. R Development Core Team (2012).
R: A language and environment for statistical
computing. R Foundation for Statistical
Computing, Vienna, Austria. ISBN 3-90005107-0, URL http://www.R-project.org/. 3.
http://yihui.name/knitr/ 4.
http://daringfireball.net/projects/markdown/
5.
https://bitbucket.org/rivanvx/beamer/wiki/H
ome
41 - Reproducible research applied to
cheminformatics experiments
Paul J Kowalczyk,
[email protected], Department of
Computational Chemistry, SCYNEXIS, Research
Triangle Park, NC 27709-2878, United States
Gentleman and Temple Lang1 define
reproducible research as “¼research papers
with accompanying software tools that allow
the reader to directly reproduce the results
and employ the methods that are presented
in the research paper.” We demonstrate how
one might report cheminformatics
experiments as instances of reproducible
research, i.e.,how one might author and
distribute integrated dynamic documents that
contain the text, code, data and any auxiliary
content needed to recreate the
computational results. We show how the
contents of these documents, including
figures and tables, can be recalculated each
time the document is generated. Opensource tools are used for all document
generation: the R software environment2 is
used to process chemical structures and mine
and analyze biological and chemical data; the
knitr3 package is used to generate reports
(PDF); the markdown4 package is used to
generate valid (X)HTML content; and the
beamer5 package is used to create slides for
presentation. Specific examples are
presented for the visualization, analysis and
mining of publicly available antimalarial
datasets, with particular attention paid to
46 - Reverse pharmacognosy: From
molecules to active ingredients
Quoc Tuan Do,
[email protected], Sylvain
Blondeau, Philippe Bernard.
Chemoinformatics, Greenpharma S.A.S.,
Orleans, Loiret 45100, France
A huge amount of data has been generated
by decades of pharmacognosy supported by
the rapid evolution of chemical, biological and
computational techniques. How can we cope
with this overwhelming mass of information?
Reverse pharmacognosy was introduced with
this aim in view. It proceeds from natural
molecules to organisms that contain them via
biological assays in order to identify an
activity. In silico techniques and particularly
inverse screening are key technologies to
achieve this goal efficiently. Reverse
pharmacognosy allows us to identify which
molecule(s) from an organism is(are)
responsible for the biological activity and the
biological pathway(s) involved. An exciting
outcome of this approach is that it not only
provides evidence of the biological properties
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Chemical Information Bulletin Vol. 65(1) Spring 2013
of plants but can also be applied to
compounds from other sources. Thus, reverse
pharmacognosy allows to accelerate the R&D
of active molecules and ingredients.
In order to find new bitterness blockers and
sweetness enhancers, a virtual screening
strategy was implemented using ligand-based
(pharmacophore, similarity) and proteinbased (docking) approaches. A database of
known blockers and enhancers were gathered
from the scientific literature and from
Robertet Flavors in-house data along with
important targets involved in the sensing of
the two tastes eg T1R, T2R... Several
candidates were identified and the most
promising ones in terms of potential activity,
safety, patentability and industrialization
were further evaluated on a panel of tasters
according to DIN 10955: 2004-06 standards.
59 - From studying block copolymers to
chemical information: A journey of an
alternative chemistry career as an academic
science librarian
Vincent F Scalfani, [email protected],
University Libraries, The University of
Alabama, Tuscaloosa, AL 35487, United States
Unbeknownst to many chemistry graduate
students, crucial skills relevant to a career in
science informatics, information technology
and librarianship are acquired daily while
working on their dissertations - both in and
outside of the laboratory. For example,
planning synthetic routes, analyzing data
trends, and writing technical papers all
require information seeking skills. This
presentation will highlight how to transition
from the laboratory to the library, as well as
how Chemists can bring a fresh perspective to
the Library. My personal journey of
transitioning from studying block copolymer
nanomaterials as a Ph.D. Chemistry student
to working as the new Science Librarian at the
University of Alabama will be used as one
example of how to make this transition. In
addition, projects started in my first year at
the University of Alabama Rodgers Science
and Engineering Library will be discussed.
67 - Navigation through chemogenomics
data with SPID
Austin B Yongye1, José L Medina-Franco2,
[email protected]. (1) Torrey
Pines Institute for Molecular Studies, Port St.
Lucie, Florida 34987, United States, (2)
Department of Physicochemistry, Universidad
Nacional Autonoma de Mexico, Mexico City,
Mexico
Chemogenomics data sets play a central role
in current drug discovery endeavors including
polypharmacology and drug repurposing
projects. In this work, we present a general
method to systematically analyzing the
structure-activity relationships of a large
screening profile data with emphasis on
identifying structural changes that have a
significant impact on the number of proteins
to which a compound binds. At the core of
this approach is the Structure-Promiscuity
Index Difference (SPID) metric that captures
differences in the number of proteins bound
related to changes in molecular structure. The
SPID measure is inspired by the StructureActivity Landscape Index (SALI) measure
commonly used in activity landscape
modeling. We discuss applications of this
approach to mine a public data set of more
than 15,000 compounds from different
66 - From virtual screening to real taste
modulators: Bitter blockers and sweetness
enhancers
Quoc Tuan Do2,
[email protected], Terry L.
Peppard1, John Scire1, Philippe Bernard2. (1)
Robertet Flavors, Inc., Piscataway, New Jersey
08854, United States, (2) Chemoinformatics,
Greenpharma S.A.S., Orleans, Loiret 45100,
France
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Chemical Information Bulletin Vol. 65(1) Spring 2013
sources screened across 100 sequenceunrelated proteins.
ChEMBL (http://www.ebi.ac.uk/chembl) is a
database of bioactive drug-like small
molecules, which has seen rapid growth in
content since its first release three years ago.
The focus of the talk will be to provide an
overview of new freely available tools and
services developed by the ChEMBL group,
which can be used to link chemical data to
biological resources. An example of such a
service is UniChem, which is an independent
InChi-based cross-referencing service, used to
create links to external resources (e.g. PDBe).
We have also developed some new domainfocused portals for integration of ChEMBL
data with comparative genomics data (e.g.
Ensembl) and consequent differences in
ADME properties. Further advances in
creating links from the ChEMBL database
have been made with the first official release
of the ChEMBL-RDF data model. This
transformation has made it possible to link to
and query data stored in other RDF models
(e.g. Gene Expression Atlas).
68 - Inferring odor detection threshold (ODT)
using chemical structure based properties
Jae Hong Shin, [email protected],
Sebastian E. Ahnert, David J. Wild, Yong-Yeol
Ahn. School of Informatics and Computing,
Indiana University, Bloomington, IN 47408,
United States
The odor detection threshold (ODT) of a
molecule is the lowest concentration of the
molecule that can be detected by human
olfactory perception. Although large amounts
ODT measurement data exist, it is not yet
clear whether it is possible to computationally
predict ODT values from the physico-chemical
properties of molecules. In this study, we aim
to build a model that predicts ODT values
using molecular physico-chemical descriptors.
We use a random forest regression model for
350 odor molecules with physico-chemical
molecular descriptors and other metadata.
We obtained the correlation coefficient
R2=0.76, and 2-fold cross validated R2= 0.64
between the observed and predicted ODTs.
When metadata is removed in order to build
a pure molecular descriptor based model, the
correlation coefficient, R2=0.63, and 2-fold
cross validation values of R2=0.40 are
obtained. Finally, we apply this model in
order to build a generalized predictive model
for a very large odor threshold data set
containing 1885 ODT values.
72 - About the impact of open access
bioassay data on cheminformatic
approaches
Barbara Zdrazil,
[email protected], Gerhard F.
Ecker. Department of Medicinal Chemistry,
University of Vienna, Vienna, Austria A-1090,
Austria
As a consequence of open innovation
initiatives, modern drug discovery now
includes the use of open access databases for
the retrieval of small compound bioactivity
data. However, we recently showed for
human P-glycoprotein, that an uncritical
interpretation of such data will lead to
datasets of poor quality due to the existence
of a broad range of various assay types and
setups used for determining the bioactivities
[1]. Thus, a broad annotation of bioassay data
will be needed, especially considering timely
multi-targeted approaches in drug design.
70 - ChEMBL tools and services: Creating
bridges between cheminformatics and
bioinformatics
Mark Davies, [email protected], Louisa J.
Bellis, A. Patricia Bento, Jon Chambers, Anna
Gaulton, Anne Hersey, Yvonne Light, George
Papadatos, John P. Overington. ChEMBL
Group, EMBL-European Bioinformatics
Institute, Cambridge, United Kingdom
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Going further, we are now studying the
neurotransmitter sodium symporter family of
proteins, trying to systematically structure
available assays (e.g.: 311 different assay-ID's
in ChEMBL database with approx. 6000
reported IC50 or Ki values targeting human
serotonin transporter) and find out how
different assays can be combined with each
other. The goal is to build up high-quality
predictive datasets further useful in
cheminformatics. The research leading to
these results has received support from the
Innovative Medicines Initiative Joint
Undertaking under Grant Agreement n°
115191 (Open PHACTS), resources of which
are composed of financial contribution from
the European Union's Seventh Framework
Programme (FP7/2007-2013) and EFPIA
companies' in kind contribution. [1] Zdrazil B,
Pinto M, Vasanthanathan P, Williams AJ,
Zander Balderud L, Engkvist O, Chichester C,
Hersey A, Overington JP, and Ecker GF,
Annotating human P-glycoprotein bioassay
data, Mol. Inf. 2012, 31(8), 599-609.
diverse information at this scale, tracking data
deposition and update, providing easy access
and data analysis tools to the community all
present great challenges to the PubChem
project. This talk provides an overview of the
development of the BioAssay resource and
describes bioassay data models as well as the
information system for storing, retrieving and
analyzing the bioactivity data.
84 - Open PHACTS: Meaningful linking of
preclinical drug discovery knowledge
Egon L Willighagen1,
[email protected],
Christian Brenninkmeijer2, Chris T Evelo1, Lee
Harland3, Alasdair J.G. Gray2, Carole Goble2,
Andra Waagmeester1, Antony J Williams4. (1)
Department of Bioinformatics - BiGCaT,
Maastricht University, Maastricht, The
Netherlands, (2) University of Manchester,
Manchester, United Kingdom, (3) Connected
Discovery Ltd, London, United Kingdom, (4)
ChemSpider, Royal Society of Chemistry,
Wake Forest, United States
80 - PubChem BioAssay: A public database
for chemical biology data
Yanli Wang, [email protected],
National Library of Medicine (NLM), National
Center for Biotechnology Information (NCBI),
National Institutes of Health (NIH), Bethesda,
Maryland 20894, United States
Recently, semantic web technologies have
been adopted by the life sciences community
for this purpose. However, while these new
technologies provide us with methods, they
do not provide us with an exact solution.
Open PHACTS uses these methods to solve
problems in linking preclinical knowledge
from databases like Uniprot, ChEMBL, and
WikiPathways. Problems that are discussed
and for which our solutions will be presented
include: 1. approaches to map data between
the databases using the Vocabulary of
Interlinked Dataset, including identifier
mapping with BridgeDB, appropriate choices
of mapping predicates, and ontologies to
cover provenance, such as the Provenance
Authoring and Versioning ontology; 2. deal
with different units for experimental data
using the Quantities, Units, Dimensions and
Data (QUDT) ontology for (on the fly) quantity
The PubChem BioAssay database
(http://pubchem.ncbi.nlm.nih.gov) is a public
repository for archiving biological test results
for small molecules and RNAi reagents. The
Bioactivity data in PubChem are generated by
HTS screenings, medical chemistry studies,
chemical biology experiments as well as by
literature extraction projects. The database
currently contains 600,000 bioassay
depositions, 2.7 million substances, eight
thousand protein targets, thirty thousand
gene targets, and 190 million bioactivity
outcomes. Managing the rich and extremely
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Chemical Information Bulletin Vol. 65(1) Spring 2013
conversion; and 3. how all this is linked to
user-oriented graphical user interfaces.
chemist. These include automated systems
for the identification of chemically relevant
articles for excerption, taxonomies to support
the organization of data, innovative quality
assurance tools, and new technologies for the
classification of substances and reactions.
89 - Making hidden data discoverable: How
to build effective drug discovery engines?
Sebastian Radestock,
[email protected], Jürgen SwientyBusch. Elsevier Information Systems GmbH,
Frankfurt am Main, Hessen 60486, Germany
96 - Intuitive and integrated browsing of
reactions, structures, and citations: The
Roche experience
Fausto Agnetti1, Michael Bensch1, Hermann
Biller1, Martin Blapp1, Ben Cheikh2, Gerd
Blanke1, Joerg Degen1, Bernard Dienon1,
Thomas Doerner1, Gunther Doernen1, Frieda
Farshchian1, Werner Gotzeina1, Peter Hilty1,
Ralf Horstmoeller1, Thomas Jeker1, Brian
Jones1, Michael Kappler2,
[email protected], Aslam Momin2,
Antonio Regoli1, Denis Ribaud1, Bernard
Starck1, Daniel Stoffler1, Klaus Weymann1,
Padmanabha Udupa2. (1) Pharma Research
and Early Development, F. Hoffmann-La
Roche Ltd., Basel, Basel-Stadt 4070,
Switzerland, (2) Pharma Research and Early
Development, Hoffmann-La Roche Inc.,
Nutley, New Jersey 07110, United States
In a complex IT environment comprising
dozens if not hundreds of databases and
likely as many user interfaces it becomes
difficult if not impossible to find all the
relevant information needed to make
informed decisions. Historical data get lost,
not normalized data cannot be compared and
maintenance becomes a nightmare. We will
discuss a new approach to address this issue
by showing various examples and use cases
on how in-house data and public data can be
integrated in various ways to address the
unique and individual needs of companies to
keep the competitive edge.
92 - Chemical science that underpins the
Reaxys database
Juergen Swienty-Busch1, [email protected], Pieder Caduff2, David
Evans2. (1) Elsevier Information Systems
GmbH, Frankfurt, Germany, (2) Reed Elsevier
Properties SA, Neuchatel, Switzerland
Roche has integrated propriety reaction
information within the Elsevier Reaxys
product, which will run on Roche's
infrastructure and inside the Roche firewall to
provide high performance and security. The
incorporation and discoverability of
proprietary information along with public
information significantly improves
productivity. With this development, Roche
researchers are able to launch a single search
in Reaxys across integrated internal data and
experimental data published in journals and
patents, with results unified and organized in
a context directly relevant to the researcher
workflow. Key points of ELN integration, data
modeling, and reaction canonicalization will
be discussed.
The chemical literature is increasing year on
year. New journals are launched, and existing
journals broaden and deepen their coverage.
Researchers are increasingly pressurized to
maintain an overview of the literature while
also finding those data most relevant to
them. Providing relevant and accurate
information is of fundamental importance.
Reaxys strives to provide chemistry
researchers with timely, accurate, organized
and relevant information. We will discuss the
recent advances we have made in order to
support the daily workflow of a research
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Spassov, Lisa Yan. Department of LS Modeling
and Simulations, Accelrys, San Diego, CA
92121, United States
101 - ALOHA-MPS: A novel compound
scoring and selection tool
Rishi R Gupta1, [email protected],
Steven W Muchmore1, Derek A Debe2, Philip J
Hajduk1. (1) Department of Cheminformatics,
Abbott Laboratories, Abbott Park, IL 60064,
United States, (2) Department of Scientific
Informatics, Abbott Laboratories, Abbott Park,
IL 60064, United States
Understanding the effects of mutation on
protein stability and protein binding affinity is
an important component of successful
protein design. In silico approaches to predict
the effects of amino acid mutations can be
used to guide experimental design and help
reduce the cost of bringing biotherapeutics or
new protein molecules (e.g. enzymes) to
market. We have developed a number of
novel methods for fast computational
mutagenesis of proteins which can be applied
to calculate the energy effect of mutation on
protein stability, and on protein-protein
binding affinity with an optional pH
dependency calculation. Here, we will present
those methods and associated validation
results. Furthermore, we will provide a case
study using a set of engineered antibodies
that have altered pH-selective binding. These
demonstrate how binding to either neonatal
receptor (FcRn) or to their target antigens can
be modified to tune their half-life in the host
system.
In the last decade or so, there has been a
significant development in the technology
that provides a wealth of experimental in-vivo
and in-vitro data. This data not only covers
toxicity and ADME endpoints but also
includes a multiple pharmacokinetic and
pharmacodynamic properties as well. The
surge in data has led to better methodologies
by which project teams pick the best
compounds to nominate as clinical
candidates. However without a sophisticated
tool it is difficult to make sense of each data
point and the wealth of data challenges
teams to focus simultaneously on all
properties at the simultaneously. We have
developed a probabilistic multi-parametric
scoring methodology using data based on
Abbott's proprietary in-vivo and in-vitro assay
data as well as in silico ADMET models. This
method incorporates error in the data to
assign probability of success of compounds
considering multiple properties
simultaneously. We have used TIBCO Spotfire
to deploy this tool to the Abbott Discovery
community as an easy to use GUI as well as it
has very useful visualizations to support
decision making process. This talk will focus
on the technology and how it has enabled
medicinal chemists in making better informed
data driven decisions.
110 - Advanced structural modeling of
biologics with BioLuminate
David A Pearlman, Tyler Day, Kathryn Loving,
David Rinaldo, Noeris Salam, Dora
Warshaviak, Kai Zhu, Woody Sherman,
[email protected].
Schrodinger, New York, NY 10036, United
States
The field of biologics continues to grow in
importance in the pharmaceutical industry.
To address the increasing need for
computational tools to model biologics we
have developed BioLuminate, which contains
a broad range of task-driven applications
tailored specifically to the field of biologics.
Our objective was to blend an easy-to-use
interface with state of the art molecular
109 - Novel in silico prediction algorithms for
the design of stable and more effective
proteins
Francisco G Hernandez-Guzman,
[email protected], Velin
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Chemical Information Bulletin Vol. 65(1) Spring 2013
simulations and de novo prediction tools. In
this presentation, we describe the philosophy
behind the design of BioLuminate and then
focus on distinguishing features of the
product, such as protein-protein docking with
Piper, de novo antibody loop modeling with
Prime, estimation of residue mutation effects,
prediction of stabilizing mutations,
determination of aggregation hotspots, and
other distinguishing features of the product.
We conclude by describing the primary
challenges in the field and our research
efforts to address them.
topological pharmacophores by means of
association rule mining and protocols for data
visualizations are made freely available as
scripts written in the Python and R
programming languages.
119 - Lexichem: Not another chemical
nomenclature app
Edward O Cannon,
[email protected], OpenEye
Scientific Software, Santa Fe, NM 87508,
United States
A novel, fast, easy to use desktop application
has been developed for Lexichem[1],
OpenEye's chemical nomenclature
software[2]. The desktop application offers
the ability to extract chemical names and
structures from patents, to easily visualize
chemical structures by dragging and dropping
files plus numerous other
features.[EdwardCannon_ACSNewOrleansIma
ge1.png] [1] E. O. Cannon, “ New Benchmark
for Chemical Nomenclature Software ” , J.
Chem. Inf. Model., 2012, 52 (5),pp 1124-1131
[2] Headquarters, OpenEye Scientific
Software, 9 Bisbee Court, Suite D, Santa Fe,
NM 87508
118 - Mining frequent itemsets: Constructing
topological pharmacophores using
pharmacophore feature pairs
Paul J Kowalczyk,
[email protected], Department of
Computational Chemistry, SCYNEXIS, Research
Triangle Park, NC 27709-2878, United States
We have adopted association rule mining to
the task of topological (2D) pharmacophore
construction. Association rule mining is a
popular and well researched statistical
approach for discovering interesting
relationships between variables in large
datasets. This approach finds joint values of
variables that appear most frequently in a
dataset. In this study, these variables are
topological pharmacophore feature pairs
(e.g., hydrogen bond donors, hydrogen bond
acceptors, hydrophobes, aromatic rings,
positive centers, negative centers) and the
corresponding bond distances between them.
Measures of significance and interest are
used to score these joint pharmacophore
feature pairs, with high scores identifying
candidate topological pharmacophores. We
demonstrate the construction of topological
pharmacophores using publicly available
antimalarial datasets. We also show how
these topological pharmacophores may be
leveraged as data mining and data
visualization tools. The construction of
Tuesday, April 9, 2013
Linking Bioinformatic Data and
Cheminformatic Data - AM Session
Morial Convention Center
Room: 349
Ian Bruno, John Overington, Organizers
Ian Bruno, Presiding
8:15 am - 11:55 am
8:15 - Introductory Remarks
8:20 - 69 - Integrating chemical and
biological structural information
Gary Battle, [email protected], Jose Dana,
Saqib Mir, Tom Oldfield, Sameer Velankar,
99
Chemical Information Bulletin Vol. 65(1) Spring 2013
Gerard Kleywegt. The European
Bioinformatics Institute, The Protein Data
Bank in Europe, Wellcome Trust Genome
Campus, Hinxton, Cambridge CB10 1SD,
United Kingdom
biological resources. An example of such a
service is UniChem, which is an independent
InChi-based cross-referencing service, used to
create links to external resources (e.g. PDBe).
We have also developed some new domainfocused portals for integration of ChEMBL
data with comparative genomics data (e.g.
Ensembl) and consequent differences in
ADME properties. Further advances in
creating links from the ChEMBL database
have been made with the first official release
of the ChEMBL-RDF data model. This
transformation has made it possible to link to
and query data stored in other RDF models
(e.g. Gene Expression Atlas).
The Protein Data Bank (PDB) is the single
worldwide repository of 3D structures of
biological macromolecules and includes over
14,000 distinct ligands bound to proteins or
nucleic acids. These structures are central to
our understanding of biochemical processes
and define the link between chemistry and
biological macromolecules. The Protein Data
Bank in Europe (PDBe; pdbe.org) is a core
resource at the European Bioinformatics
Institute (EBI) and a founding member of the
Worldwide Protein Data Bank (wwPDB;
wwpdb.org). This talk will review ongoing
efforts at the PDBe to provide consistent
mappings between macromolecular structure
data and important biological and chemical
data resources at the EBI. We will also discuss
freely available web tools for mining and
analysing the wealth of structural information
available in the PDB using familiar biological
or chemical terminology and classifications.
9:10 - 71 - Pharmacological profiling of drugs
by linking chemoinformatics and
bioinformatics data
Olivier Taboureau, [email protected],
Department of Systems Biology - Center for
Biological Sequences Analysis, Technical
University of Denmark, Lyngby, Denmark
The pharmacological profiling of drugs is
crucial in drug discovery. With the increasing
availability of data from the”-omics”
technologies and the development of
computational approaches to analyze this
massive amount of data, it is now possible, in
academia, to evaluate the drug safety and the
drug pharmacology not only at the molecular
level but also at the biological systems level.
Integration of chemical biology data and
monitoring the perturbations at the pathway,
cellular, tissue and systems level would
improve the global understanding of the
compound effects in human health.
Furthermore, clinical effects might be critical
for the identification of genes that are
important modulators of drug response,
namely pharmacogenetics. With the
integration of several and diverse biological
data, we will discuss how the linking of
chemoinformatics and bioinformatics can
contribute to the translational informatics
8:45 - 70 - ChEMBL tools and services:
Creating bridges between cheminformatics
and bioinformatics
Mark Davies, [email protected], Louisa J.
Bellis, A. Patricia Bento, Jon Chambers, Anna
Gaulton, Anne Hersey, Yvonne Light, George
Papadatos, John P. Overington. ChEMBL
Group, EMBL-European Bioinformatics
Institute, Cambridge, United Kingdom
ChEMBL (http://www.ebi.ac.uk/chembl) is a
database of bioactive drug-like small
molecules, which has seen rapid growth in
content since its first release three years ago.
The focus of the talk will be to provide an
overview of new freely available tools and
services developed by the ChEMBL group,
which can be used to link chemical data to
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Chemical Information Bulletin Vol. 65(1) Spring 2013
research by providing a deeper understanding
of the drugs effects in drug discovery.
Hersey A, Overington JP, and Ecker GF,
Annotating human P-glycoprotein bioassay
data, Mol. Inf. 2012, 31(8), 599-609.
9:35 - 72 - About the impact of open access
bioassay data on cheminformatic
approaches
Barbara Zdrazil,
[email protected], Gerhard F.
Ecker. Department of Medicinal Chemistry,
University of Vienna, Vienna, Austria A-1090,
Austria
10:00 - Intermission
10:15 - 73 - Biological target identification
through combination of 3D molecular
similarity and lexical similarity of clinical
effects
Emmanuel R Yera, [email protected], Ann E
Cleves, Ajay N Jain, [email protected].
Department of Bioengineering and
Therapeutic Sciences, UCSF, San Francisco, CA
94158, United States
As a consequence of open innovation
initiatives, modern drug discovery now
includes the use of open access databases for
the retrieval of small compound bioactivity
data. However, we recently showed for
human P-glycoprotein, that an uncritical
interpretation of such data will lead to
datasets of poor quality due to the existence
of a broad range of various assay types and
setups used for determining the bioactivities
[1]. Thus, a broad annotation of bioassay data
will be needed, especially considering timely
multi-targeted approaches in drug design.
Going further, we are now studying the
neurotransmitter sodium symporter family of
proteins, trying to systematically structure
available assays (e.g.: 311 different assay-ID's
in ChEMBL database with approx. 6000
reported IC50 or Ki values targeting human
serotonin transporter) and find out how
different assays can be combined with each
other. The goal is to build up high-quality
predictive datasets further useful in
cheminformatics. The research leading to
these results has received support from the
Innovative Medicines Initiative Joint
Undertaking under Grant Agreement n°
115191 (Open PHACTS), resources of which
are composed of financial contribution from
the European Union's Seventh Framework
Programme (FP7/2007-2013) and EFPIA
companies' in kind contribution. [1] Zdrazil B,
Pinto M, Vasanthanathan P, Williams AJ,
Zander Balderud L, Engkvist O, Chichester C,
We have previously demonstrated a
probabilistic framework for combining
information regarding protein-ligand
interactions in order to identify off-targets for
drugs through a combination of 3D molecular
similarity, 2D molecular similarity, and
docking computations. We have extended our
framework to include a novel lexical method
for computing the similarity between small
molecules based on data derived from patient
package inserts (PPI). Small molecules that
are pharmacologically described in a similar
fashion often share underlying protein targets
(e.g. antagonism of the muscarinic receptor
can cause dry mouth and urinary retention).
By combining information from molecular
similarity and from lexical similarity of a
particular drug to a set of drugs sharing a
known biological target, it is possible to gain
synergy from the combination of orthogonal
information sources in order to propose new
putative targets for the drug. The results of a
systematic application to a large set of drugs
will be presented along with a critical analysis
examining what can be learned about drug
pharmacology based on different molecular
similarity methods and natural language
descriptions of pharmacology.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
10:40 - 74 - In silico prediction of gene
expression profiles for drug-like compounds
based on their structural formulae
Alexey Lagunin, [email protected],
Sergey Ivanov, Anastassia Rudik, Dmitry
Filimonov, Vladimir Poroikov. Bioinformatics,
Orekhovich Institute of Biomedical Chemistry
of Russian Academy of Medical Sciences,
Moscow, Russian Federation
CAS has mined its intellectually-assigned
controlled vocabulary terms to create
bioactivity indicators (e.g., antibiotic,
antidepressant) and protein target indicators
(e.g., alpha-amylase, prostate-specific
antigen) that link molecular substances with
biological effects and protein targets.
Scientists working at the interface of
chemistry and biology can search the CAS
databases for drug leads to quickly discover
other therapeutic indications and associated
protein targets. With more than 260
bioactivity indicators and 5800 target
indicators assigned to millions of substances,
medicinal chemists can efficiently assess the
biological relevance of a large group of
molecules. This presentation will illustrate
how these relationships are developed, how
false positives are avoided, and end with
some examples of how these new terms are
used in SciFinder®.
Drug-induced gene expression profile is a
major determinant of drug action on cell.
Experimentally determined profiles are used
to solve different problems in drug
development and clinical practice such as
drug repositioning and resistance, toxicity and
drug-drug interactions (DDI). The information
about drugs' influence on gene expression is
freely available from the Comparative
Toxicogenomics Database
(http://ctdbase.org/). We used this data for
training and validation of computer system to
perform qualitative prediction of gene
expression profiles of drugs based on their
structural formulae. SAR models were created
using PASS software that we develop and
update for about 20 years
(http://www.pharmaexpert.ru/PASSOnline).
A freely available web-service for prediction
of drug-induced gene expression profiles has
been developed
(http://www.pharmaexpert.ru/GE). Predicted
gene expression profiles can be used for
analysis of drug resistance, drug synergistic
effects and DDI. The work was partially
supported by RFBR/NIH grant No 12-0491445-NIH_A/RUB1-31081-MO-12, and RFBR
grant No 12-07-00597-а.
11:30 - 76 - Jikitou biomedical question
answering system: Using multiple resources
to answer biomedical questions
Michael A. Bauer1,2, [email protected],
Robert E. Belford3, Daniel Berleant1, Roger A.
Hall1. (1) Department of Information Science,
University of Arkansas at Little Rock, Little
Rock, AR 72204, United States, (2) Joint
Bioinformatics Program, University of
Arkansas for Medical Sciences, Little Rock, AR
72204, United States, (3) Department of
Chemistry, University of Arkansas at Little
Rock, Little Rock, AR 72204, United States
Intelligent information retrieval systems that
summarize relevant textual information while
incorporating multiple sources of information
can assist researchers in dealing with
information and data challenges at the
interface of biological and chemical sciences.
Question answering (QA) is a specialized type
of information retrieval with the aim of
returning short answers to queries posed as
11:05 - 75 - CAS’ bioactivity and target
indicators provide new insights for scientists
working at the interface of chemistry and
biology
Roger Schenck, [email protected],
Department of Marketing, Chemical Abstracts
Service, Columbus, Ohio 43202, United States
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Chemical Information Bulletin Vol. 65(1) Spring 2013
natural language questions. We have
developed a QA system, Jikitou
(www.jikitou.com), which answers natural
language questions with sentences taken
from Medline abstracts that are parsed using
a multiple agent search strategy. The answers
that are returned are sent to the
WikiHyperGlossary (hyperglossary.org) where
terms associated with a glossary are linked to
additional sources of information such as the
UniprotKB protein information database,
ChemSpider or the RCSB Protein Data Bank.
Jikitou combines multiple natural language
processing techniques, data resources and
technologies to create a unique system to
help researchers navigate the huge and
growing biomedical textome.
PubChem system and detail new ways
PubChem is providing for and adapting to the
needs of the community.
9:05 - 78 - NCI/CADD chemical structure Web
services
Markus Sitzmann, [email protected],
Alexey V. Zakharov, Laura Guasch Pàmies,
Marc C. Nicklaus. Chemical Biology
Laboratory, Center for Cancer Research,
Frederick National Laboratory for Cancer
Research, National Cancer Institute, National
Institutes of Health, DHHS, Frederick, MD
21702, United States
Over the course of the last 15 years, the
NCI/CADD group has made publicly available
a series of small molecule-centric Web
services and databases at their Web server,
http://cactus.nci.nih.gov, e.g., the Chemical
Structure Lookup Service (CSLS), the Chemical
Identifier Resolver (CIR), and the NCI
Enhanced Database Browser. We present an
overview over recent work on a tighter
integration of these resources, on
improvements of the programmatic
accessibility as well as on a better usability
with mobile and touchscreen devices.
Furthermore, we will discuss recent
enhancement of our Chemical Structure
DataBase (CSDB) which is used as central data
repository for all of our services. The most
recent versions of CSDB indexes approx. 300
million chemical structure records
representing about approx. 120 million
unique chemical structures. We will also
present a new Web service allowing for the
prediction of physicochemical and biological
properties of small molecules.
Tuesday, April 9, 2013
Public Databases Serving the Chemistry
Community - AM Session
Morial Convention Center
Room: 350
Antony Williams, Sean Ekins, Organizers
Sean Ekins, Presiding
8:30 am - 11:55 am
8:30 - Introductory Remarks
8:35 - 77 - PubChem: A community driven
resource
Evan Bolton, [email protected],
PubChem, NCBI / NLM / NIH, United States
PubChem is an open repository for chemical
biology information and recently celebrated
its 8th year of existence. Despite humble
beginnings, PubChem continues to receive
broad community support through a
continued influx of new information and new
information resource types. As the needs of
the community have changed, so too has
PubChem adapted. This talk will provide an
overview of recent significant changes to the
9:35 - 79 - ChemSpider: Disseminating data
and enabling an abundance of chemistry
platforms
Antony J Williams1, [email protected], Valery
Tkachenko1, Ken Karapetyan1, Alexey
Pshenichnov1, Dmitry Ivanov1, Colin
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Batchelor2, Jon Steele2, David Sharpe2. (1)
Cheminformatics, Royal Society of Chemistry,
Wake Forest, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom
and data analysis tools to the community all
present great challenges to the PubChem
project. This talk provides an overview of the
development of the BioAssay resource and
describes bioassay data models as well as the
information system for storing, retrieving and
analyzing the bioactivity data.
ChemSpider is one of the chemistry
community's primary public compound
databases. Containing tens of millions of
chemical compounds and its associated data
ChemSpider serves data to many tens of
websites and software applications at this
point. This presentation will provide an
overview of the expanding reach of the
ChemSpider platform and the nature of
solutions that it helps to enable. We will also
discuss some of the future directions for the
project that are envisaged and how we intend
to continue expanding the impact for the
platform.
10:50 - 81 - Chemistry-related resources at
the Protein Data Bank in Europe
Gary Battle, [email protected], Gerard
Kleywegt, Sameer Velankar, Tom Oldfield,
Swanand Gore, Saqib Mir, Jose Dana. The
European Bioinformatics Institute, Protein
Data Bank in Europe, Wellcome Trust Genome
Campus, Hinxton, Cambridge CB10 1SD,
United Kingdom
The 3-dimensional structures of proteinligand complexes determined using X-ray
diffraction provide a window into the world
of protein structure and function. The Protein
Data Bank is the single worldwide repository
of 3D structures of biological macromolecules
and includes over 14,000 distinct ligands
bound to proteins or nucleic acids.
Information on the geometry of these small
molecules and their interactions with proteins
are crucial to our understanding of
biochemical processes and are vital for
structure-based drug design. The Protein Data
Bank in Europe (PDBe; pdbe.org) is a core
resource at the EBI and a founding member of
the Worldwide Protein Data Bank (wwPDB;
wwpdb.org). This talk will review the freely
available chemistry-related resources
provided by PDBe. We will also discuss recent
initiatives to assess and improve the quality
of ligands in the PDB archive and continuing
efforts to help chemists understand how to
retrieve and interpret 3D structural
information.
10:05 - Intermission
10:20 - 80 - PubChem BioAssay: A public
database for chemical biology data
Yanli Wang, [email protected],
National Library of Medicine (NLM), National
Center for Biotechnology Information (NCBI),
National Institutes of Health (NIH), Bethesda,
Maryland 20894, United States
The PubChem BioAssay database
(http://pubchem.ncbi.nlm.nih.gov) is a public
repository for archiving biological test results
for small molecules and RNAi reagents. The
Bioactivity data in PubChem are generated by
HTS screenings, medical chemistry studies,
chemical biology experiments as well as by
literature extraction projects. The database
currently contains 600,000 bioassay
depositions, 2.7 million substances, eight
thousand protein targets, thirty thousand
gene targets, and 190 million bioactivity
outcomes. Managing the rich and extremely
diverse information at this scale, tracking data
deposition and update, providing easy access
11:20 - 82 - Architecture for an open science
molecular compound database
Egon L Willighagen,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
[email protected],
Department of Bioinformatics - BiGCaT,
Maastricht University, Maastricht, The
Netherlands
PubChem is an open repository for chemical
biology information. PubChem contains a
wealth of information including more than
100 million substance descriptions, 35 million
unique small molecules, and 200 million
biological testing result outcomes from more
than 200 contributors. PubChem chemical
structures link to 40% of the known
biomedical literature and more than 10% of
all biologically tested molecules have links to
the patent literature. Given the combinatoric
count of “links” available in PubChem
enabling access to such information by
utilization of ontologies (e.g., ChEBI, GO, BAO,
etc.) and classification schemes (MeSH,
LipidMaps, KEGG BRITE, etc.) is providing new
ways to effectively navigate such information.
This talk will detail some of the new ways
PubChem is organizing and providing links to
the chemical biology community.
The past few years has seen a tremendous
leap forward in public compound databases.
However, the exact Open nature of “public”
database is not always crystal clear, on, for
example, how the Open Data parts of public
databases can be used, modified, and
redistributed, the three corner stones of
Open Science. We present an architecture
where semantic web technologies, the InChI,
and cheminformatics tools are used to create
a Panton Principles-compliant compound
database. Standards proposed in the Open
PHACTS community will be use to specify links
between this new resource and other
databases, and to provide compound
properties. All this input will be available with
provenance on the origin of that data, as
separate downloadable files, and using
ontologies to provide explicit meaning. Using
ontologies like ChEBI and CHEMINF,
applications in the areas of metabolomics and
toxicology will be presented.
2:20 - 84 - Open PHACTS: Meaningful linking
of preclinical drug discovery knowledge
Egon L Willighagen1,
[email protected],
Christian Brenninkmeijer2, Chris T Evelo1, Lee
Harland3, Alasdair J.G. Gray2, Carole Goble2,
Andra Waagmeester1, Antony J Williams4. (1)
Department of Bioinformatics - BiGCaT,
Maastricht University, Maastricht, The
Netherlands, (2) University of Manchester,
Manchester, United Kingdom, (3) Connected
Discovery Ltd, London, United Kingdom, (4)
ChemSpider, Royal Society of Chemistry,
Wake Forest, United States
11:50 - Concluding Remarks
Tuesday, April 9, 2013
Linking Bioinformatic Data and
Cheminformatic Data - PM Session
Morial Convention Center
Room: 349
Recently, semantic web technologies have
been adopted by the life sciences community
for this purpose. However, while these new
technologies provide us with methods, they
do not provide us with an exact solution.
Open PHACTS uses these methods to solve
problems in linking preclinical knowledge
from databases like Uniprot, ChEMBL, and
WikiPathways. Problems that are discussed
and for which our solutions will be presented
Ian Bruno, John Overington, Organizers
John Overington, Presiding
1:55 pm - 5:30 pm
1:55 - 83 - Linking chemical biology
information within PubChem
Evan Bolton, [email protected],
PubChem, NCBI / NLM / NIH, United States
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Chemical Information Bulletin Vol. 65(1) Spring 2013
include: 1. approaches to map data between
the databases using the Vocabulary of
Interlinked Dataset, including identifier
mapping with BridgeDB, appropriate choices
of mapping predicates, and ontologies to
cover provenance, such as the Provenance
Authoring and Versioning ontology; 2. deal
with different units for experimental data
using the Quantities, Units, Dimensions and
Data (QUDT) ontology for (on the fly) quantity
conversion; and 3. how all this is linked to
user-oriented graphical user interfaces.
Domains covered: bioactivity, small molecule,
chemical properties and chemotype.
3:10 - 86 - Roundtripping between smallmolecule and biopolymer representations
Noel M O'Boyle1,
[email protected], Evan Bolton2,
Roger A Sayle1. (1) NextMove Software,
Cambridge, United Kingdom, (2) National
Center for Biotechnology Information,
Bethesda, Maryland MD 20894, United States
Existing cheminformatics toolkits provide a
mature set of tools to handle small-molecule
data, from generating depictions, to creating
and reading linear representations (such as
SMILES and InChI). However, such tools do
not translate well to the domain of
biopolymers where the key information is the
identity of the repeating unit and the nature
of the connections between them. For
example, a typical all-atom 2D depiction of all
but the smallest protein or oligosaccharide
obscures this key structural information.
We describe a suite of tools which allow
seamless interconversion between
appropriate structure representations for
small molecules and biopolymers (with a
focus on polypeptides and oligosaccharides).
For example: SMILES:
OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO
)OC([C@@H]([C@H]2O)NC(=O)C)O)[C@@H]([
C@H]([C@H]1O)O[C@@]1(C[C@H](O)[C@H](
[C@@H](O1)[C@@H]([C@@H](CO)O)O)NC(=
O)C)C(=O)O)O Shortened IUPAC format:
NeuAc(a2-3)Gal(b1-4)GlcNAc
I will discuss the challenge of supporting a
variety of biopolymer representations,
handling chemically-modified structures, and
handling biopolymers with unknown
attachment points (e.g. from mass
spectrometry).
2:45 - 85 - Extracting more value from data
silos: Using the semantic web to link
chemistry and biology for innovation
Derek Scuffell1, [email protected],
Philip Ashworth2. (1) R&D, Syngenta,
Bracknell, Berks RG42 6ET, United Kingdom,
(2) Top Quadrant, London, United Kingdom
In order to maximize the chances of finding
novel crop protection molecules, that are safe
for the environment, it is necessary to bring
together biological and chemical information
from both inside and outside of an
organisation. The integarted use of biological
data can help eliminate false positive
molecular candidates and improve the
chances of finding the correct candidates for
development. Information about the
Biological activity of compounds is captured
in disparate systems within Syngenta and in
the public domain. This presenation will show
how highly curated bioactivity data from
ChEMBL was linked to the Syngenta corporate
chemical catalogue, along with other
Syngenta research data and commercial
patents indexes, using the Resource
Description Framework (RDF). The resulting
linked data was then used to support mode of
action, spectrum and selectivity competency
questions used in herbicide discovery. This is
great example of using a semantic web
approach to link biological activity data with
cheminfomatics data to ease research. Data
3:35 - Intermission
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Chemical Information Bulletin Vol. 65(1) Spring 2013
3:50 - 87 - Representing and registeristing
antibody-drug conjugates
Keith T Taylor, [email protected],
Burton L Leland, William L Chen, Young-Mi
Kwon. Accelrys Inc, San Ramon, California
98543, United States
drug development compounds have
traditionally been kept in other databases
outside of notebooks. Such results normally
follow an assay centric hierarchy which
conflicts with the experiment hierarchy within
notebooks. To provide true property based,
cross-experiment search, results must be
transcribed or mapped through the creation
of SQL queries. This limits the flexibilityadding new assays require programing, adhoc querying is impaired. This presentation
will describe a new methodology and
architecture that allows the benefit of a
structured assay based hierarchy within a
familiar experiment based hierarchy. Merging
this assay information with chemical property
data, and the ease of exposing this data to
visualization and data mining tools without
the use of SQL, will be explored.
Biologics are providing a large and growing
contribution to drug pipelines. The majority
of biologic based therapies include significant
chemical modifications. Antibody-drug
conjugates (ADC) are the major focus. ADCs
have the most challenging representation
needs, with modified residues, custom linkers
to the drug payload, and variable levels of
glycosylation. In particular the payload is
attached statistically to the available sites in
the antibody. Variable attachment to
cysteines brings an added complication; the
payload is attached to reduced cysteines
while the unloaded cysteines retain disulfide
bridges. These issues will be discussed and a
representation that allows the capture of
ADCs with variable loading will be described.
This representation enables the registration
and retrieval of ADCs, supports substructure
searches, and captures the sequence and
chemical modifications, and the correct
formula and formula weight. Activity profiles
for a series of ADCs can be compared
facilitating optimization.
4:40 - 89 - Making hidden data discoverable:
How to build effective drug discovery
engines?
Sebastian Radestock,
[email protected], Jürgen SwientyBusch. Elsevier Information Systems GmbH,
Frankfurt am Main, Hessen 60486, Germany
In a complex IT environment comprising
dozens if not hundreds of databases and
likely as many user interfaces it becomes
difficult if not impossible to find all the
relevant information needed to make
informed decisions. Historical data get lost,
not normalized data cannot be compared and
maintenance becomes a nightmare. We will
discuss a new approach to address this issue
by showing various examples and use cases
on how in-house data and public data can be
integrated in various ways to address the
unique and individual needs of companies to
keep the competitive edge.
4:15 - 88 - Mining chemical and biological
data for trends: Visualizing structured
numeric data from ELNs
Philip J Skinner,
[email protected], Phil McHale,
Amy Kallmerton, Megean Schoenberg, Anis
Khimani, Kate Blanchard, Michael Swartz.
Informatics, PerkinElmer, Cambridge, MA
02140, United States
Scientists have always kept notebooks - they
are the natural place to record information
about experiments. However, structured data
such as biological assay results captured on
5:05 - 90 - Applying the law of parsimony in
molecular design
Alberto Del Rio, [email protected],
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Department of Experimental, Diagnostic and
Specialty Medicine (DIMES), University of
Bologna, Bologna, Bologna 40126, Italy
dissemination
Julien C Thibault1, [email protected],
Thomas E Cheatham2,3, Julio C Facelli1,3. (1)
Department of Biomedical Informatics,
University of Utah, Salt Lake City, Utah 84112,
United States, (2) Department of Medicinal
Chemistry, University of Utah, Salt Lake City,
Utah 84112, United States, (3) Center for
High-Performance Computing, University of
Utah, Salt Lake City, Utah 84112, United
States
Molecular design has not only the ambition to
explain and answer fundamental biological
questions but also to find new chemical tools
that can be effectively used to interfere with
physiological and pathological networks.
Several techniques belonging to different
disciplines, like a broad range of computeraided techniques, chemical data mining,
bioinformatics and methods from statistics to
artificial intelligence, are currently used to
guide and speed-up the early-stage
development of new bioactive components.
This massive amount of techniques, aiming at
linking chemical and biological data, has
multiplied research efforts, but raised the
question whether new applications may
result in over-complicated and
compartmentalized research paradigms. On
the other hand, some examples highlight the
usage of parsimonious models but their
application in all the steps of moleculardesign is far from being trivial. Here we
present examples and suggest practical
possibilities to emphasize the adoption of the
lex parsimonae principle for linking biological
and chemical data in molecular design.
With the recent advances in hardware, it is
now possible to run complex Molecular
Dynamics simulations and to reach time
scales that are biologically significant. Each
run can easily generate TeraBytes of data on
disk, usually distributed among multiple
remote resources, requiring new methods for
data storage, management, and tracking. Our
current efforts include the development of
new tools to index and present biomolecular
simulation data at different levels of
granularity: the local directory where data is
stored, at the storage resource level, and
eventually at the global level, involving
multiple resources distributed across
institutions. At the directory level, file parsers
for popular MD and QM packages (e.g.
AMBER, Gaussian) can be used to generate
experiment summaries and file descriptions
as text, XML, or HTML. These descriptors are
stored at the root of the directory containing
the data for a particular experiment. They
provide a quick summary of the experiment
that was run and the files that are present in
the folder. For the resource level indexing we
developed a simple web interface (iBIOMES
Lite) automatically populated by existing
descriptors generated at the lower level.
Actual data files are not made readable,
except for analysis summaries, such as plots
or 3D structure snapshots. The aim of this
tool is to provide easy access to experiment
summaries and latest data analysis results,
not only to the owner of the data but also to
Tuesday, April 9, 2013
Public Databases Serving the Chemistry
Community - PM Session
Morial Convention Center
Room: 350
Antony Williams, Sean Ekins, Organizers
Antony Williams, Presiding
2:00 pm - 5:25 pm
2:00 - Introductory Remarks
2:05 - 91 - Local and remote tracking of
molecular dynamics data for global
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Josef Eiblmaier, Peter Loew. InfoChem GmbH,
Munich, Germany
other group members. Finally, at the global
level, experiments and related files can be
registered into a large-scale distributed
system: iBIOMES (integrated BIOMolEcular
Simulations). Registered data can be queried
among multiple resources using experiment
metadata (e.g. method parameters, forcefield, residue chain). Both simulation input
and output files can be made available for
download, either for data dissemination
within a collaborative network or for public
access.
With the acquisition of the SPRESI database in
1989, which at that time contained 1.8 million
reactions, InfoChem was forced to conceive
concepts for the selection of meaningful
subsets of reaction databases. Based on a
high quality reaction center detection module
(ICMAP), InfoChem developed a sophisticated
reaction type classification application
(CLASSIFY) that is still unique to this day.
Using CLASSIFY and applying tailored filters
on reaction attributes like yield, relevance of
journal, and number of examples per
ClassCode, InfoChem generated ChemReact, a
subset of the SPRESI data collection. This
database contains over 524,000 unique
reactions, each of them representing one
distinct reaction type. With the development
of the free iPad and iPhone app, InfoChem
decided to make ChemReact publicly
available free of charge. This talk will briefly
outline the history of the database and
present the free app SPRESImobile that
enables easy and intuitive access to this
valuable data collection.
2:35 - 92 - Chemical science that underpins
the Reaxys database
Juergen Swienty-Busch1, [email protected], Pieder Caduff2, David
Evans2. (1) Elsevier Information Systems
GmbH, Frankfurt, Germany, (2) Reed Elsevier
Properties SA, Neuchatel, Switzerland
The chemical literature is increasing year on
year. New journals are launched, and existing
journals broaden and deepen their coverage.
Researchers are increasingly pressurized to
maintain an overview of the literature while
also finding those data most relevant to
them. Providing relevant and accurate
information is of fundamental importance.
Reaxys strives to provide chemistry
researchers with timely, accurate, organized
and relevant information. We will discuss the
recent advances we have made in order to
support the daily workflow of a research
chemist. These include automated systems
for the identification of chemically relevant
articles for excerption, taxonomies to support
the organization of data, innovative quality
assurance tools, and new technologies for the
classification of substances and reactions.
3:35 - Intermission
3:50 - 94 - Navigating between patents,
papers, abstracts, and databases using public
sources and tools
Christopher Southan1, Sean Ekins2,
[email protected]. (1) Department of
Informatics, ChrisDS Consulting, Göteborg,
Vastra Götland 41266, Sweden, (2)
Collaborations in Chemistry, Fuquay-Varina,
NC 27526, United States
Engaging with chemistry in the biosciences
requires navigation between journals,
patents, abstracts, databases, Google results
and connecting across millions of structures
specified only in text. The ability to do this in
public sources has been revolutionised by
3:05 - 93 - ChemReact: A free database
containing more than 524,000 reactions
available at your fingertips
Valentina Eigner-Pitto, [email protected],
Hans Kraut, Heinz Saller, Heinz Matuszczyk,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
several trends a) ChEMBL's capture of SAR
from journals c) the deposition of three major
automated patent extractions (SureChem,
IBM and SCRIPDB) in PubChem for over 15
million structures, d) open tools such as
chemicalize.org, OPSIN, and OSCAR that
enable the conversion of IUPAC names or
images to structures e) the indexing of
chemical terms (e.g. InChIKeys) that turn
Google searches into a merged global
repository of 40 to 50 million structures.
Details of these trends, including PubChem
intersect statistics, will be presented, along
with practical examples from selected tools.
New structure sharing trends will also be
considered such as patent crowdsourcing,
dropbox, blogs, figshare and open lab
notebooks.
ChemSpider Reactions as an integrating hub
of content including data extracted from US
patents, from RSC Journals and databases and
from our micro-publishing platform
ChemSpider Synthetic Pages (CSSP).
4:50 - 96 - Intuitive and integrated browsing
of reactions, structures, and citations: The
Roche experience
Fausto Agnetti1, Michael Bensch1, Hermann
Biller1, Martin Blapp1, Ben Cheikh2, Gerd
Blanke1, Joerg Degen1, Bernard Dienon1,
Thomas Doerner1, Gunther Doernen1, Frieda
Farshchian1, Werner Gotzeina1, Peter Hilty1,
Ralf Horstmoeller1, Thomas Jeker1, Brian
Jones1, Michael Kappler2,
[email protected], Aslam Momin2,
Antonio Regoli1, Denis Ribaud1, Bernard
Starck1, Daniel Stoffler1, Klaus Weymann1,
Padmanabha Udupa2. (1) Pharma Research
and Early Development, F. Hoffmann-La
Roche Ltd., Basel, Basel-Stadt 4070,
Switzerland, (2) Pharma Research and Early
Development, Hoffmann-La Roche Inc.,
Nutley, New Jersey 07110, United States
4:20 - 95 - ChemSpider reactions: Delivering
a free community resource of chemical
syntheses
Valery Tkachenko1, [email protected],
Colin Batchelor2, Ken Karapetyan1, David
Sharpe2, Antony J Williams1. (1)
Cheminformatics, Royal Society of Chemistry,
Wake, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom
Roche has integrated propriety reaction
information within the Elsevier Reaxys
product, which will run on Roche's
infrastructure and inside the Roche firewall to
provide high performance and security. The
incorporation and discoverability of
proprietary information along with public
information significantly improves
productivity. With this development, Roche
researchers are able to launch a single search
in Reaxys across integrated internal data and
experimental data published in journals and
patents, with results unified and organized in
a context directly relevant to the researcher
workflow. Key points of ELN integration, data
modeling, and reaction canonicalization will
be discussed.
There are dozens of public compound
databases now available online, some of
these providing access to tens of millions of
chemical compounds. However, very little
effort has been put into the delivery of
databases of chemical reactions with the
majority of large resources being commercial
in nature. In our five years of delivering
chemical based data resources to the
chemistry community one of the primary
requests has been that chemists want to
know how to synthesize many of the
chemicals they are researching. This
presentation will provide an overview of our
concerted efforts to enhance access to freely
available chemistry data and will discuss the
5:20 - Concluding Remarks
110
Chemical Information Bulletin Vol. 65(1) Spring 2013
Wednesday, April 10, 2013
74% of marketed CNS drugs displayed a high
desirability score (>4, using a scale of 0-6). In
addition, a relationship between an
increasing desirability score and alignment of
key in vitro ADME and safety attributes was
seen in the marketed CNS drug set, the Pfizer
candidate set, and a Pfizer proprietary
diversity set. The CNS MPO Desirability score
is thus an algorithm in the medicinal
chemistry toolbox that may be used
prospectively at the design stage to
accelerate the identification of compounds
with increased probability of success.
Furthermore, application of this tool to new
clinical drug candidates has challenged the
long-held notion that CNS molecules need to
be highly lipophilic with low polar surface
area, moving the CNS design field in a new
direction.
Balancing Chemistry on the Head of a Pin:
Multi-Parameter Optimization - AM Session
Morial Convention Center
Room: 349
Edmund Champness, Matthew Segall,
Organizers
Edmund Champness, Matthew Segall,
Presiding
8:30 am - 11:50 am
8:30 - Introductory Remarks
8:35 - 97 - Exploiting a more polar property
space in the design of brain penetrant
molecules
Anabella Villalobos,
[email protected], Travis T
Wager, Xinjun J Hou, Patrick R Verhoest.
Department of Neuroscience Medicinal
Chemistry, Pfizer Inc., 700 Main Street,
Cambridge, MA 02139, United States
9:05 - 98 - Multi-criteria drug discovery:
Recent results in building predictive models,
combining predictions, and generating new
chemistry ideas
Brian B Masek, [email protected],
Fabian Boes, Richard Cramer, Roman
Dorfman, Stephan Nagy, Lei Wang, Bernd
Wendt. Certara USA, Inc., Saint Louis, Mo
63144, United States
In our efforts to increase the survival of drug
candidates, we undertook a detailed study of
the chemical space for Central Nervous
System (CNS) molecules. Ultimately, we were
interested in optimizing the number of design
cycles and in vivo toxicology testing needed
to advance candidates from idea to proof of
concept clinical studies. We focused on
understanding the relationships between
physicochemical properties, in vitro
absorption, distribution, metabolism, and
excretion (ADME) and safety attributes, and
binding efficiencies for over 200 marketed
CNS drugs and Pfizer CNS candidates. This
analysis together with medicinal chemistry
knowledge was used to create and validate a
prospective design tool which used an overall
desirability score for drug-likeness. The novel
CNS multi-parameter optimization desirability
(CNS MPO Desirability) algorithm, based on
six physicochemical parameters, showed that
A successful drug candidate will need to
overcome a variety of hurdles, including
adequate potency and selectivity, as well as
acceptable ADME, physical, and safety
properties. This presents several challenges to
discovery scientists: • Understanding and
balancing the competing SAR's for each of the
multiple criteria a successful drug candidate
must meet • How to create predictive models
for ALL of the parameters relevant to
successful clinical outcome? • How to identify
the scaffolds and R-groups that will optimize
or satisfy the potency, selectivity, physical
properties, ADME properties and safety
profile? Examples will be presented to show
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Chemical Information Bulletin Vol. 65(1) Spring 2013
how modern CADD methods are addressing
these challenges.
statistic is relevant, this is relatively
straightforward. In many cases, however, it is
not clear a priori which criterion should
dominate and this problem becomes one of
multi-parameter optimization. Here we
investigate the effect of manipulating the
balance between sensitivity and specificity on
the overall performance of artificial neural
net ensemble (ANNE) classification models
and present a Pareto approach to integrating
alternative performance criteria for them.
9:35 - 99 - Implementation of multi-criteria
decision making (MCDM) tools in early drug
discovery processes
Marie Ledecq, [email protected], UCB
NewMedicines, UCB Pharma, Braine-l'Alleud,
Belgium
The current trend in medicinal chemistry is to
focus on high quality ligands from the early
beginning of the drug design process in order
to reduce the drug attrition rate in later
stages. Based on this assessment, medicinal
chemistry practices are evolving; starting
from potency centered drug design strategies
towards a much more integrated vision
where critical properties have to be optimized
in parallel. From this perspective, some
specific MCDM tools can be used to discover
better balanced lead compounds. These tools
include the use of Derringer's desirability
functions, and Pareto front based optimizers.
In this presentation, it will be shown how
these tools can be implemented to be used at
several levels of the drug design process: to
follow project progression and take
enlightened decisions about series, and to
help in the data analysis and the design of
new compounds.
10:50 - 101 - ALOHA-MPS: A novel compound
scoring and selection tool
Rishi R Gupta1, [email protected],
Steven W Muchmore1, Derek A Debe2, Philip J
Hajduk1. (1) Department of Cheminformatics,
Abbott Laboratories, Abbott Park, IL 60064,
United States, (2) Department of Scientific
Informatics, Abbott Laboratories, Abbott Park,
IL 60064, United States
In the last decade or so, there has been a
significant development in the technology
that provides a wealth of experimental in-vivo
and in-vitro data. This data not only covers
toxicity and ADME endpoints but also
includes a multiple pharmacokinetic and
pharmacodynamic properties as well. The
surge in data has led to better methodologies
by which project teams pick the best
compounds to nominate as clinical
candidates. However without a sophisticated
tool it is difficult to make sense of each data
point and the wealth of data challenges
teams to focus simultaneously on all
properties at the simultaneously. We have
developed a probabilistic multi-parametric
scoring methodology using data based on
Abbott's proprietary in-vivo and in-vitro assay
data as well as in silico ADMET models. This
method incorporates error in the data to
assign probability of success of compounds
considering multiple properties
simultaneously. We have used TIBCO Spotfire
to deploy this tool to the Abbott Discovery
10:05 - Intermission
10:20 - 100 - Being suitably sensitive:
Balancing competing performance criteria
for in silico models
Robert D Clark, [email protected],
Marvin Waldman, Jinhua Zhang, Adam C. Lee,
Michael S. Lawless. Simulations Plus, Inc.,
Lancaster, CA 93534, United States
Given the large number of descriptors and
modeling tools available, identifying the
“best” model from among several can be
bewildering. When only one performance
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Chemical Information Bulletin Vol. 65(1) Spring 2013
community as an easy to use GUI as well as it
has very useful visualizations to support
decision making process. This talk will focus
on the technology and how it has enabled
medicinal chemists in making better informed
data driven decisions.
Antony Williams, Sean Ekins, Organizers
Antony Williams, Sean Ekins, Presiding
8:30 am - 11:55 am
8:30 - Introductory Remarks
8:35 - 103 - Universal SMILES: Finally, a
canonical SMILES string?
Noel M O'Boyle, [email protected],
Analytical and Biological Chemistry Research
Facility, University College Cork, Cork, Co.
Cork, Ireland
11:20 - 102 - Finding multi-parameter rules
for successful optimization
Matthew Segall, [email protected],
Iskander Yusof, Edmund Champness.
Optibrium Ltd., Cambridge, ... CB25 9TL,
United Kingdom
The SMILES line notation is widely used for
storage and interchange of chemical
structures. Although for a single structure
many different SMILES strings may be
written, most cheminformatics toolkits
provide the ability to generate a canonical
SMILES representation so that the same
structure will always yield the same SMILES
string. Unfortunately there is no standard way
to generate canonical SMILES and different
toolkits generate different canonical SMILES
for the same structure.
Another widely used line notation is the InChI
identifier, which provides a canonical
identifier for chemical structures. I describe
how to use the InChI's canonical labels to
derive a canonical SMILES string in a
straightforward way, either incorporating the
InChI normalisations (Inchified SMILES) or not
(Universal SMILES). I discuss the performance
of these methods on a test set of compounds
from PubChem and ChEMBL, the challenges
remaining, and the benefits to the community
of a standard method of generating canonical
SMILES.
Multi-parameter optimization (MPO) is
increasingly used in drug discovery to
prioritize compounds against a profile of
properties required for success. But, how do
we know what profile to use? The property
criteria will depend on the ultimate objective
of the project and are typically based on the
subjective opinion of the project team. In this
presentation we will describe computational
approaches, described as rule induction, that
guide this process by analysing historical data.
These identify objective multi-parameter
rules that distinguish successful compounds
for a chosen goal, e.g. efficacy,
pharmacokinetics or safety. The resulting
rules are interpretable and modifiable,
allowing experts to understand and adjust
them based on their knowledge of the
underlying biology and chemistry.
Furthermore, the importance of each
criterion can be identified, allowing the most
critical data to be prioritized in order to make
effective compound selection decisions.
9:05 - 104 - Analysis of tautomerism in
databases of commercially available
compounds
Laura Guasch, [email protected], Markus
Sitzmann, Marc C Nicklaus. Chemical Biology
Laboratory, Center for Cancer Research,
Frederick National Laboratory for Cancer
Wednesday, April 10, 2013
Public Databases Serving the Chemistry
Community - AM Session
Morial Convention Center
Room: 350
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Research, National Cancer Institute, National
Institutes of Health, DHHS, Frederick,
Maryland 21702, United States
in a database is gone and quality-conscious
databases need to heavily rely on automated
validation checks . An automated chemical
validation system is being developed by the
cheminformatics team at the Royal Society of
Chemistry to be the “quality gatekeeper” of
databases at the point of deposition.
ChemSpider is leading a community-wide
standardization approach starting with our
support of the Open PHACTS semantic web
project, an Innovative Medicines Initiative.
The Chemical Validation and Standardization
Platform (CVSP) is being designed as an open,
flexible chemical validation and
standardization platform that validates and
standardizes chemical records. This
presentation will review the existing beta
version of the system and work in progress.
We have conducted a tautomerism analysis in
a large database of commercially available
compounds. The goal of this analysis is twofold: to investigate how many cases of the
same chemical being sold as different
products (at possibly different prices) may
occur in aggregated screening sample
databases; and to test the tautomerism
definition of the widely used
chemoinformatics toolkit CACTVS. We applied
the default CACTVS transforms to the publicly
accessible Aldrich Market Select (AMS)
database from ChemNavigator/Sigma-Aldrich,
which currently comprises over 8 million
unique chemicals available from hundreds of
suppliers worldwide. We found thousands of
cases where at least two products listed as
different compounds in the AMS were
declared as tautomeric forms of the same
compound by CACTVS. We report on our
efforts to address the question of the true
tautomeric overlap by selecting a number of
tautomer pairs (or larger tuples) from the
AMS, and analyzing their structural identity or
difference by, e.g., NMR.
10:05 - Intermission
10:20 - 106 - Challenges and
recommendations for obtaining chemical
structures of industry-provided repurposing
candidates
Christopher Southan1, Anthony J Williams2,
Sean Ekins3, [email protected]. (1)
ChrisDS Consulting, Göteborg, Sweden, (2)
Royal Society of Chemistry, Wake Forest, NC
27587, United States, (3) Collaborations in
Chemistry, Fuquay-Varina, NC 27526, United
States
9:35 - 105 - RSC chemical validation and
standardization platform: A potential path to
quality-conscious databases
Ken Karapetyan1, [email protected],
Valery Tkachenko1, Colin Batchelor2, David
Sharpe2, Antony Williams1. (1)
Cheminformatics, Royal Society of Chemistry,
Wake Forest, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom
There is an expanding interest in drug
repurposing and optimizing in silico methods
to assist this. Recent repurposing project
tendering calls by the National Center for
Advancing Translational Sciences (US) and the
Medical Research Council (UK) have included
compound information and pharmacological
data. However, none of the internal company
development code names were assigned to
chemical structures in the official
documentation. This not only abrogates in
silico analysis but also necessitates arduous
data gathering to assign structures. We
High quality chemical databases are
struggling with protecting their data from the
flow of wild machine-generated chemistry
and lower-quality data. The period of
primarily human curation prior to deposition
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Chemical Information Bulletin Vol. 65(1) Spring 2013
describe here the methods results and
challenges associated with this, as well as the
in silico predictions for mapped structures.
Because ~40% of the code names remain
completely blinded we suggest ways by which
their structure mappings could be released
earlier into the public domain and with more
uniform provenance.
device (e.g. smartphone, tablet). For vertical
markets such as the pharmaceutical industry,
it is easy for these specialized apps to be lost
in the forest of consumer oriented apps. In
order to address this problem, and many
others, the Pistoia Alliance has undertaken
the task of building a storefront dedicated
exclusively to apps for life sciences R&D. The
advantages of an industry-specific storefront
are many: the selection of apps is tightly
focused (hundreds rather than hundreds of
thousands) and the curation criteria are
based on the needs of the industry. The
Pistoia Alliance AppStore is supported by
active discussion forums, and the ability of
vendors to contact the users of their products
is a key differentiator, compared to the
anonymity of general purpose appstores.
Apps are available for both iOS and Android
devices, and the apps can be made available
for free, or licenses can be negotiated directly
between vendors and customers without
incurring a toll. This presentation will discuss
the benefits of the new appstore, and some
of the early experiences and lessons learned
during its implementation. The Pistoia
Alliance is also working with TM Forum to
augment its appstore with serverside support,
which is intended to allow apps to make use
of large datasets and intensive calculations
using a secure cloud-hosted environment.
Progress towards the design and construction
of this service will be described.
10:50 - 107 - One size fits all or how to find
the needle in the haystack?
Juergen Swienty-Busch, [email protected], Elsevier Information
Systems GmbH, Frankfurt, Germany
In an ever growing and dynamic information
environment proprietary and public
information, free services and paid services
live next to each other making it a very
difficult task to navigate in a landscape of
patchwork information resources to find
trusted and reliable information to finally
make informed decisions. Increasing pressure
is put on scientists to stay up to date with the
latest information in a given research domain
and they are looking for systems which
answer their questions quickly and precisely.
We will describe a system, which addresses
these needs by applying an optimized
computer-aided abstraction process and by
being able to integrate other data sources
and present use cases and applications.
11:20 - 108 - Pistoia Alliance AppStore: Apps
for life sciences R&D
Alex M Clark, [email protected], R&D,
Molecular Materials Informatics, Montreal,
Quebec H3J2S1, Canada
11:50 - Concluding Remarks
Wednesday, April 10, 2013
Computational De novo Protein and Peptide
Design - PM Session
Morial Convention Center
Room: 349
Cosponsored by COMP
The recent industry trend toward
"appification" of software is starting to affect
the domain of life sciences R&D. This involves
the reimagining of conventional
cheminformatics and bioinformatics tools and
repackaging them as modular apps designed
to provide optimal functionality on a mobile
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Chemical Information Bulletin Vol. 65(1) Spring 2013
States
Rachelle Bienstock, Organizers
Rachelle Bienstock, Presiding
1:30 pm - 3:10 pm
The field of biologics continues to grow in
importance in the pharmaceutical industry.
To address the increasing need for
computational tools to model biologics we
have developed BioLuminate, which contains
a broad range of task-driven applications
tailored specifically to the field of biologics.
Our objective was to blend an easy-to-use
interface with state of the art molecular
simulations and de novo prediction tools. In
this presentation, we describe the philosophy
behind the design of BioLuminate and then
focus on distinguishing features of the
product, such as protein-protein docking with
Piper, de novo antibody loop modeling with
Prime, estimation of residue mutation effects,
prediction of stabilizing mutations,
determination of aggregation hotspots, and
other distinguishing features of the product.
We conclude by describing the primary
challenges in the field and our research
efforts to address them.
1:30 - Introductory Remarks
1:45 - 109 - Novel in silico prediction
algorithms for the design of stable and more
effective proteins
Francisco G Hernandez-Guzman,
[email protected], Velin
Spassov, Lisa Yan. Department of LS Modeling
and Simulations, Accelrys, San Diego, CA
92121, United States
Understanding the effects of mutation on
protein stability and protein binding affinity is
an important component of successful
protein design. In silico approaches to predict
the effects of amino acid mutations can be
used to guide experimental design and help
reduce the cost of bringing biotherapeutics or
new protein molecules (e.g. enzymes) to
market. We have developed a number of
novel methods for fast computational
mutagenesis of proteins which can be applied
to calculate the energy effect of mutation on
protein stability, and on protein-protein
binding affinity with an optional pH
dependency calculation. Here, we will present
those methods and associated validation
results. Furthermore, we will provide a case
study using a set of engineered antibodies
that have altered pH-selective binding. These
demonstrate how binding to either neonatal
receptor (FcRn) or to their target antigens can
be modified to tune their half-life in the host
system.
2:35 - 111 - Virtual mutagenesis for
optimizing antibody binding affinity: A
prospective study
Enrico O. Purisima, [email protected],
Vivcharuk Victor, Traian Sulea, Denis L'Abbé,
Yves Durocher, Jason Baardsnes, Maureen
O'Connor. Human Health and Therpeutics
Portfolio, National Research Council of
Canada, Montreal, Quebec H4P 2R2, Canada
Antibodies are emerging as an important new
class of therapeutics that offers many
advantages over small-molecule drugs.
However, raising antibodies in animals
requires a significant investment in resources
and time with limited control over the
definition of epitopes targeted or the level of
binding affinities obtained. Computer-aided
molecular design has the potential to speed
up the process of affinity maturation. We
used virtual mutagenesis to redesign an
2:10 - 110 - Advanced structural modeling of
biologics with BioLuminate
David A Pearlman, Tyler Day, Kathryn Loving,
David Rinaldo, Noeris Salam, Dora
Warshaviak, Kai Zhu, Woody Sherman,
[email protected].
Schrodinger, New York, NY 10036, United
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Chemical Information Bulletin Vol. 65(1) Spring 2013
existing antibody that has dual weak affinities
to VEGF-A and HER2. We used a combination
of three methods - SIE, FoldX and Rosetta - to
design sequences for improved affinities.
Forty antibody mutants, each containing up
to 4 amino acid mutations, were designed.
These were cloned and expressed and their
affinities measured by SPR. We will discuss
the results of this study and the implications
for computational approaches to virtual
affinity maturation.
retrosynthesis unnecessary, yet generates
new chemical entities whilst maintaining the
physico-chemical properties of the query
compounds the same. Thus, activity is likely
to be similar, but the hit compound will likely
enter a different area of chemical space. This
screening workflow can be easily set up in
one of the popular workflow tools KNIME or
PipelinePilot and taking full advantage of the
synergy between functionality available from
within and the embedded software itself. The
presentation will highlight a few example
workflows for both KNIME and PipelinePilot
as well as the scientific background of the
software used within.
3:00 - Concluding Remarks
Wednesday, April 10, 2013
Advances in Virtual High-Throughput
Screening - PM Session
Morial Convention Center
Room: 350
2:00 - 113 - New targets addressed by
DEKOIS 2.0: Demanding evaluation kits for
objective in-silico screening
Frank M. Boeckler, [email protected], Matthias R Bauer, Tamer M. I.
M. Abdelrehim, Simon M. Vogel. Department
of Pharmacy &Biochemistry, Eberhard Karls
University, Tuebingen, Germany
Joel Freundlich, Sean Ekins, Organizers
Sean Ekins, Presiding
1:30 pm - 4:50 pm
1:30 - Introductory Remarks
With DEKOIS we have created an automated
workflow to efficiently generate decoy sets
based on a certain number of actives for any
targets. Physico-chemical similarity should be
maximized between decoys and actives in
order to yield challenging sets for
benchmarking, while exact mimicking of
potentially active substructures should be
avoided to omit latent actives in the decoy set
(LADS). Overall, the diversity of actives and
decoys should be maximized to avoid artifacts
based on clusters. Applying this philosophy,
we have added more details to describe the
physicochemical space and applied this
protocol to generate sets for targets which
had not been accessible before. These DEKOIS
2.0 sets are available online
(www.dekois.com) for benchmarking and
development of new tailored scoring
functions. Further extension toward
additional targets can facilitate a systematic
1:35 - 112 - Setting up a discovery pipeline in
KNIME and PipelinePilot: High-throughput
de novo design utilizing gigantic virtual
chemistry spaces
Carsten Detering, [email protected],
BioSolveIT Inc, Bellevue, WA 98008, United
States
Today's drug discovery is under a lot of
pressure. Crowded patent space, tightened
regulation by the FDA, and increased risk
putting compounds in the clinic call for new
pathways into unexplored and moreover
larger areas of chemical space. The increased
need for synthetically viable compounds has
rendered de novo design difficult, up until
recently. With this contribution we present a
way to explore new chemical space utilizing
existing in-house chemistry that renders
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Alabama at Birmingham, Birmingham, AL
35294-1240, United States, (5) Department of
Medicine, Center for Emerging and
Reemerging Pathogens, UMDNJ – New Jersey
Medical School, Newark, NJ 07103, United
States, (6) Colorado State University,
Colorado, CO 80523, Afghanistan, (7)
Department of Pharmacology &Physiology,
UMDNJ, Newark, NJ 07103, United States
comparison of the virtual screening
performance of docking tools and scoring
functions in a target dependent way.
2:25 - 114 - PubChem3D: A virtual screening
platform
Evan Bolton, [email protected],
PubChem, NCBI / NLM / NIH, United States
Virtual screening is a critical component of
drug discovery to the reduce cost of and
improve the success of a given biological
assay screening campaign. Decisions need to
be made rapidly about what compounds to
purchase or which chemicals to synthesize
from a large number of possibilities. Similarly,
one must prioritize which high throughput
screening “hits” to pursue. PubChem contains
a huge wealth of information, including data
from numerous medicinal chemistry projects
and many (if not most) of the chemicals
purchasable. Tools within PubChem (some of
which are very new) allow one to quickly
locate chemicals with similar bioactivity and
similar structural features. This talk will
provide an overview of tools oriented
towards virtual screening available in
PubChem with an emphasis on key
advancements and newly introduced
capabilities.
The identification of novel leads represents a
significant challenge in the resource-limited
setting of drug discovery. This hurdle is
magnified in neglected diseases such as
tuberculosis, characterized by ~2 million
deaths annually and a need for shorter
therapeutic regimens addressing drug
resistance. We have leveraged highthroughput screening data, a multi-year and
multi-million dollar investment by public and
private institutions, to experimentally validate
single- and dual-event Bayesian models. We
virtually screened a commercial library and
experimentally confirm actives with hit rates
exceeding typical rates by 1-2 orders of
magnitude. The first dual-event Bayesian
model identified compounds with
antitubercular whole-cell activity and low
mammalian cell cytotoxicity from a published
set of antimalarials. The most potent hit
exhibits the in vitro activity and in vitro/in
vivo safety profile of a drug lead. These
machine learning models offer significant
economies in time and cost while being
broadly applicable to drug discovery.
2:50 - Intermission
3:05 - 115 - Dual-event machine learning
models to accelerate drug discovery
Sean Ekins1,2, [email protected], Robert
C Reynolds3,4, Hiyun Kim5, Mi-Sun Koo5,
Marilyn Ekonomidis5, Meliza Talaue5, Steve
Paget5, Lisa Woolhiser6, Anne J Lenaerts6,
Barry A Bunin1, Nancy Connell5, Joel S
Freundlich5,7. (1) Collaborative Drug
Discovery, Burlingame, CA 94010, United
States, (2) Collaborations in Chemistry,
Fuquay-Varina, CA 27526, United States, (3)
Southern Research Institute, Birmingham, AL
35205, United States, (4) University of
3:30 - 116 - Virtual high-throughput
screening of novel pharmacological agents
based on PASS predictions
Vladimir V. Poroikov1,2,
[email protected], Dmitry A.
Filimonov1, Alexey A. Lagunin1, Tatyana A.
Gloriozova1, Olga A. Tarasova1, Pavel V.
Pogodin1,2, Marc C. Nicklaus3. (1) Department
for Bioinforatics, Orekhovich Institute of
Biomedical Chemistry of Russian Academy of
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Medical Sciences, Moscow, Russian
Federation, (2) Medical-Biological Faculty, The
Russian National Research Medical University
named after N.I. Pirogov, Moscow, Russian
Federation, (3) Chemical Biology Laboratory,
National Cancer Institute, National Institutes
of Health, Frederick, MD, United States
the pharmaceutical industry. 2D methods
have largely been replaced by 3D ligandbased methods and by structure-based
methods (docking) where a reliable protein
structure is available. Cresset's blaze V10
virtual screening algorithm has been shown
to significantly outperform DOCK on a wide
range of targets, both in terms of raw
enrichment rates and in terms of enrichments
of novel chemotypes. However, the cost of
calculating 3D molecular similarities is much
higher than that for 2D similarity methods,
and therefore large amounts of computing
power are needed to screen a reasonable
number of compounds on a useful time scale.
In recent years, graphical processing units
(GPUs) have become very popular for some
high performance computing applications as
they have a very good cost to performance
ratio. Various frameworks have been
developed and are now sufficiently mature to
consider using in production environments.
GPUs are therefore an ideal solution for
computationally-intense problems such as
virtual screening. In collaboration, the
University of Bristol and Cresset have ported
the blaze V10 virtual screening code to
OpenCL, a framework for writing programs
that execute across heterogeneous platforms
(both CPU and GPU). We present results
showing that the OpenCL port can provide an
up to 40-fold speed increase and more
accurate results when run on an off-the-shelf
latest generation GPU, compared to a
contemporary multi-core CPU. This not only
reduces the time required to obtain results
but also saves hardware cost and space, with
a single cheap GPU performing as well as a
cluster of dozens of CPUs. We discuss some of
the difficulties encountered in reworking the
blaze V10 algorithms to fit into a
heterogeneous computing environment,
present hardware comparisons, and give
guidance on how to maximize performance
while retaining full precision.
Among the numerous tools currently used for
virtual screening, PASS
(http://pharmaexpert.ru/passonline) occupies
a special place. PASS predicts 6400 biological
activities of drug-like compounds with a mean
accuracy of about 95%. Its training set
consists of 330,000 biologically active
compounds. Since PASS calculations for
50,000 structures take a few minutes on an
ordinary PC, PASS is applicable to chemical
libraries containing millions of compounds.
Based on PASS predictions, novel
pharmaceutical agents have been discovered
with anxiolytic, anti-inflammatory,
antihypertensive, anticancer and other
actions. To find new anticancer agents, we
have analyzed dozens of millions of structures
from ChemNavigator and selected a few
dozens for biological testing. Two out of
eleven tested compounds were found to be
potent anticancer NCEs, which are under
preclinical studies now. We also present
recent results of virtual screening for HIV-1
microbicides. Acknowledgement: This work
was partially supported by FP7 grant No.
LSHB-CT-2007-037590 and RFBR/NIH grant
No. 12-04-91445-NIH_a/RUB1-31081-MO-12.
3:55 - 117 - How GPUs can find your next hit:
Accelerating virtual screening with OpenCL
Simon Krige1, [email protected],
Mark Mackey1, Simon McIntosh-Smith2,
Richard Sessions2. (1) Cresset Biomolecular
Discovery, United Kingdom, (2) University of
Bristol, Bristol, United Kingdom
The use of virtual screening to find new hits
and leads has become commonplace within
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Chemical Information Bulletin Vol. 65(1) Spring 2013
4:20 - 118 - Mining frequent itemsets:
Constructing topological pharmacophores
using pharmacophore feature pairs
Paul J Kowalczyk,
[email protected], Department of
Computational Chemistry, SCYNEXIS, Research
Triangle Park, NC 27709-2878, United States
Jeremy Garritano, Organizers
Jeremy Garritano, Presiding
8:00 am - 10:45 am
8:00 - Introductory Remarks
8:05 - 119 - Lexichem: Not another chemical
nomenclature app
Edward O Cannon,
[email protected], OpenEye
Scientific Software, Santa Fe, NM 87508,
United States
We have adopted association rule mining to
the task of topological (2D) pharmacophore
construction. Association rule mining is a
popular and well researched statistical
approach for discovering interesting
relationships between variables in large
datasets. This approach finds joint values of
variables that appear most frequently in a
dataset. In this study, these variables are
topological pharmacophore feature pairs
(e.g., hydrogen bond donors, hydrogen bond
acceptors, hydrophobes, aromatic rings,
positive centers, negative centers) and the
corresponding bond distances between them.
Measures of significance and interest are
used to score these joint pharmacophore
feature pairs, with high scores identifying
candidate topological pharmacophores. We
demonstrate the construction of topological
pharmacophores using publicly available
antimalarial datasets. We also show how
these topological pharmacophores may be
leveraged as data mining and data
visualization tools. The construction of
topological pharmacophores by means of
association rule mining and protocols for data
visualizations are made freely available as
scripts written in the Python and R
programming languages.
A novel, fast, easy to use desktop application
has been developed for Lexichem[1],
OpenEye's chemical nomenclature
software[2]. The desktop application offers
the ability to extract chemical names and
structures from patents, to easily visualize
chemical structures by dragging and dropping
files plus numerous other
features.[EdwardCannon_ACSNewOrleansIma
ge1.png] [1] E. O. Cannon, “ New Benchmark
for Chemical Nomenclature Software ” , J.
Chem. Inf. Model., 2012, 52 (5),pp 1124-1131
[2] Headquarters, OpenEye Scientific
Software, 9 Bisbee Court, Suite D, Santa Fe,
NM 87508
8:30 - 120 - Teach our naming tool to be
bilingual: Chinese name-to-structure
conversion
David Deng, [email protected], Daniel
Bonniot. ChemAxon LLC, Cambridge, MA
02138, United States
Chinese patent filings have been on the rise
sharply during the past decade. In 2011,
China overtook the U.S. and became the
world top patent filer. Therefore, text mining
of Chinese patents, including chemical
patents, is of increasing importance. An
application to convert Chinese chemical
names to structures is urgently needed for
Chinese chemical patent analysis. ChemAxon
has developed a mature English name-to-
4:45 - Concluding Remarks
Thursday, April 11, 2013
General Papers - AM Session
Morial Convention Center
Room: 349
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Chemical Information Bulletin Vol. 65(1) Spring 2013
structure conversion tool. In this
presentation, we will demonstrate how this
tool can now convert Chinese chemical names
to structures. It has great potential to be used
in other text mining fields, e.g. to extract
chemical information from Chinese
documents and webpages.
model for RSC ChemSpider
Ken Karapetyan1, [email protected],
Valery Tkachenko1, Colin Batchelor2, David
Sharpe2, Antony J Williams1. (1)
Cheminformatics, Royal Society of Chemistry,
Wake Forest, NC 27587, United States, (2)
Cheminformatics, Royal Society of Chemistry,
Cambridge, United Kingdom
8:55 - 121 - Community based curation of
chemical images extracted using automated
routines
Valery Tkachenko1, [email protected],
Dmitry Ivanov1, Colin Batchelor2, Antony J
Williams1. (1) Cheminformatics, Royal Society
of Chemistry, Wake Forest, NC 27587, United
States, (2) Cheminformatics, Royal Society of
Chemistry, Cambridge, United Kingdom
The handling of the tautomeric
representations of small molecules is a very
complex issue but should be considered as
part of a general workflow to standardize
chemical compounds. This is a hugely
important undertaking not only from a
database registration point of view, but also
from point of view of the user who may be
interested in physicochemical properties or
virtual screening. A number of scientific
papers have investigated tautomer
enumeration with different flavors of trained
scoring algorithms. We have explored the
tautomeric space present in ChemSpider
using a few of these published approaches
and the impact on the introduction of parentchild relationships in our underlying data
model. We will report on the result of these
investigations.
In recent years there have been a number of
efforts to digitize historical data associated
with chemistry. Major scientific publishers
and patent offices have converted their
content from printed documents into images
and used optical character recognition and
conversion to text and even further into XML
marked up documents. Unfortunately a
significant fraction of published information
in chemistry discusses chemicals which are
expressed either as chemical names or as
images. While text mining and extraction for
chemical names is fairly standard chemical
image identification and processing lags
significantly. This presentation will describe
our work on chemical image recognition,
conversion and crowdsourced curation that
has been undertaken as part of a broader
effort to data enable the RSC archives. This
has included the development of a mobile
app called ChemGoggles to develop training
data sets for the optical structure recognition
algorithms.
9:55 - 123 - Structure-activity relationships of
combinatorial data sets: Rapid identification
of selectivity switches in positional scanning
libraries tested across formyl peptide
receptors
José L Medina-Franco1, [email protected],
Clemencia Pinilla2, Jon R Appel2, Marc A
Giulianotti1, Radleigh Santos1, Bruce S
Edwards3, Larry A Sklar3, Richard A
Houghten1. (1) Torrey Pines Institute for
Molecular Studies, Port St. Lucie, Florida
34987, United States, (2) Torrey Pines
Institute for Molecular Studies, San Diego,
California 92121, United States, (3) University
of New Mexico, Albuquerque, New Mexico
87131, United States
9:20 - Intermission
9:30 - 122 - Investigation of tautomerization
and its impact on the content and data
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Chemical Information Bulletin Vol. 65(1) Spring 2013
[email protected], William H. Green2.
(1) Center for Aero-Thermodynamics,
Aerodyne Research, Inc., Billerica, CT 01821,
United States, (2) Department of Chemical
Engineering, Massachusetts Institute of
Technology, Cambridge, MA 02139, United
States
We present a general approach to describe
the structure-activity relationships (SAR) of
combinatorial data sets with activity for two
biological endpoints with emphasis on the
rapid identification of substitutions that have
a large impact on the activity and selectivity.
The approach uses Dual-Activity Difference
(DAD) maps that represent a visual and
quantitative analysis of all pairwise
comparisons of one, two, or more
substitutions around a molecular template.
Scanning the SAR of data sets using DAD
maps allows the visual and quantitative
identification of selectivity switches defined
as specific substitutions that completely
invert the selectivity pattern of the
compounds against two targets. The
approach also rapidly identifies single- and
double-target R-cliffs i.e., compounds where a
single or double substitution around the core
scaffold dramatically modifies the activity for
one or two targets, respectively. In contrast
to common activity landscape methods, the
methods introduced in this work are
independent of the structure representation
and can be applied to any analogue series
with two property e.g., biological activity,
endpoints. To illustrate the approach, we
discuss the SAR of 107 pyrrolidine bisdiketopiperazines tested against two
formylpeptide receptors.
An algorithm is described for comparing two
sets of three-dimensional molecular
coordinates to assess whether they
correspond to the same conformer (within
some small tolerance). The algorithm does
not require or make use of connectivity
information, and does not require a priori
atomic correspondence information, though
it will identify one or more viable atomic
mappings if the two conformers are
equivalent within the user-specified
tolerance. In contrast to typical approaches
(e.g. Kabsch algorithm) that make use of an
RMSD metric, the algorithm uses an error
metric based on maximum deviations
between intraconformer atom-pair distances.
The algorithm scales well with molecule size,
avoiding the N! explosion of potential atomic
mappings and achieving O(N2) scaling in the
best case. Preliminary tests of the algorithm
are described. The algorithm could be used in
approaches to enumerate conformer
ensembles, and is made available on the web
through the open-source MoleCoor package.
10:20 - 124 - Algorithm for efficient
conformational equivalence testing without
a priori atomic correspondence or
connectivity information
Gregory R. Magoon1,2,
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Awards and Scholarships
Chemical Structure Association Trust
Applications Invited for CSA Trust Grants for 2014.
The Chemical Structure Association (CSA) Trust is an internationally recognized organization
established to promote the critical importance of chemical information to advances in chemical
research. In support of its charter, the Trust has created a unique Grant Program, renamed in honor
of Professor Jacques-Émile Dubois who made significant contributions to the field of
cheminformatics. The Trust is currently inviting the submission of grant applications for 2014.
Purpose of the Grants:
The Grant Program has been created to provide funding for the career development of young
researchers who have demonstrated excellence in their education, research or development
activities that are related to the systems and methods used to store, process and retrieve
information about chemical structures, reactions and compounds. A Grant will be awarded annually
up to a maximum of ten thousand U.S. dollars ($10,000). Grants are awarded for specific purposes,
and within one year each grantee is required to submit a brief written report detailing how the
grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any
paper or presentation that is given as a result of that support.
Who is Eligible?
Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information
related research and who are developing careers that have the potential to have a positive impact
on the utility of chemical information relevant to chemical structures, reactions and compounds,
are invited to submit applications. While the primary focus of the Grant Program is the career
development of young researchers, additional bursaries may be made available at the discretion of
the Trust. All requests must follow the application procedures noted below and will be weighed
against the same criteria.
Which Activities are Eligible?
Grants may be awarded to acquire the experience and education necessary to support research
activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to
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Chemical Information Bulletin Vol. 65(1) Spring 2013
one’s area of research, to gain access to special computational facilities, or to acquire unique
research techniques in support of one’s research.
Application Requirements:
Applications must include the following documentation:
1. A letter that details the work upon which the Grant application is to be evaluated as well as
details on research recently completed by the applicant;
2. The amount of Grant funds being requested and the details regarding the purpose for which the
Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support
of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s
objectives and the clarity of this statement are essential in the evaluation of the application);
3. A brief biographical sketch, including a statement of academic qualifications;
4. Two reference letters in support of the application. Additional materials may be supplied at the
discretion of the applicant only if relevant to the application and if such materials provide
information not already included in items 1-4. Three copies of the complete application
document must be supplied for distribution to the Grants Committee.
Deadline for Applications:
Applications must be received no later than March 13, 2014. Successful applicants will be notified
no later than May 2, 2014.
Address for Submission of Applications:
Three copies of the application documentation should be forwarded to: Bonnie Lawlor, CSA Trust
Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your
application by e-mail, please contact Bonnie Lawlor at [email protected] prior to submission so
that she can contact you if the e-mail does not arrive.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Chemical Structure Association Trust
Recent Jacques-Emile Dubois Grant Awardees
2012 Tu C. Le: CSIRO Division of Materials Science & Engineering, Clayton, VIV, Australia. Tu V. was
awarded the Grant for travel to attend a Cheminformatics course at Sheffield University and to visit the
Membrane Biophysics group of the Department of Chemistry at imperial College London.
2011 J. B. Brown: Kyoto University, Kyoto, Japan. J.B. was awarded the Grant for travel to work with
Professor Ernst Walter-Knappat the Freie University of Berlin and Professor Jean-Phillipe Vert of the
Paris MinesTech to continue his work on the development of atomic partial charge kernels
2010 Noel O’Boyle: University College Cork, Ireland. Noel was awarded the grant to both network and
present his work on open source software for pharmacophore discovery and searching at the 2010
German Conference on Cheminformatics.
2009 Laura Guasch Pamies: University Rovira & Virgili, Catalonia, Spain. Laura was awarded the Grant to
do three months of research at the University of Innsbruck, Austria.
2008 Maciej Haranczyk: University of Gdansk, Poland. Maciej was awarded the Grant to travel to
Sheffield University, Sheffield, UK, for a 6-week visit for research purposes.
2007 Rajarshi Guha: Indiana University, Bloomington, IN, USA. Rajarshi was awarded the Grant to
attend the Gordon Research Conference on Computer Aided Design in August 2007.
2006 Krisztina Boda: University of Erlangen, Erlangen, Germany. Krisztina was awarded the Grant to
attend the 2006 spring National Meeting of the American Chemical Society in Atlanta, GA, USA.
2005 Dr. Val Gillet and Professor Peter Willett: University of Sheffield, Sheffield, UK. They were award
the Grant for student travel costs to the 2005 Chemical Structures Conference held in Noordwijkerhout,
the Netherlands.
2004 Dr. Sandra Saunders: University of Western Australia, Perth, Australia. Sandra was awarded the
Grant to purchase equipment needed for her research.
2003 Prashant S. Kharkar: Institute of Chemical Technology, University of Mumbai, Matunga, Mumbai.
Prashant was awarded the Grant to attend the conference, Bioactive Discovery in the New Millennium,
in, Lorne, Victoria, Australia (February 2003) to present a paper, The Docking Analysis of 5Deazapteridine Inhibitors of Mycobacterium avium complex (MAC) Dihydrofolate reductase (DHFR).
2001 Georgios Gkoutos: Imperial College of Science, Technology and Medicine, Dep. of Chemistry.
London, UK. Georgios was awarded the Grant to attend the conference, Computational Methods in
Toxicology and Pharmacology Integrating Internet Resources, (CMTPI-2001) in Bordeaux, France, to
present part of his work on internet-based molecular resource discovery tools.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Product Announcements
The ACS Style Guide, Now Available Online
The ACS Style Guide is the definitive source for all information needed to write, review, submit, and
edit scholarly and scientific manuscripts. An established resource for the chemistry community, The
ACS Style Guide is not just a resource for ACS authors, but is referenced by other publishers, even
beyond chemistry, within their instructions to authors and is used as a resource in teaching
students how to effectively communicate scientific information.
The ACS Style Guide is now available online to libraries that subscribe to the ACS All Publications
Package or the Academic Core+ package. Coming soon - complimentary personal access to the
online edition will be available via the ACS ChemWorx research management platform.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
2013 is shaping up to be a great year for the RSC so far!
The National Chemical Database Service, hosted by the RSC, is now live as part of a five year
contract, funded by EPSRC http://cds.rsc.org/. Currently providing access to a series of commercial
databases and services primarily for crystallographers and materials chemists, our aim is to expand
the data sources within the NCDS so it is applicable to a wider range of chemical scientists. There
will be provision to offer users: data management, data sharing, funder mandates and open
science. We are also pleased to announce Materials Horizons, a new peer-reviewed journal for first
reports of exceptional significance across the breadth of materials research. From launch until
December 2015, all content will be free to access online, the first issue publishing in late 2013.
More information is available at rsc.li/materials-horizons. And finally...ChemSpider now has help
videos In Chinese, German, Hindi, Japanese, Russian, Spanish and Turkish. Take a look at the videos
today http://www.chemspider.com/Help.aspx.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Journal of Cheminformatics Impact Factor 3.42
2 New themed series of papers now publishing
Semantic Physical Sciences
Guest Editors:
2012 Skolnik Award winners
Peter Murray-Rust, University of Cambridge
Henry Rzepa, Imperial College London
o From an invited workshop & symposium to investigate and formalise the use of semantics in
physical sciences, applying primary technologies based on chemical mark-up language (CML)
and MathML to create fully semantic declarative scientific objects
o Publications include:
 Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
 CompChem: the semantics of CML for computational chemistry
 Chemical datuments as scientific enablers
InChI and its influence on the domain of chemical information
Guest Editor
Antony Williams, Royal Society of Chemistry
o Describing the applications and utility of the IUPAC International Chemical Identifier (InChI), and
reviewing the need for a standard identifier in chemistry, the development of InChI, and its
applications, limitations and future developments
o Publications include:
 A user’s perspective of InChI
 InChIKey collision resistance: an experimental testing
 An assessment of InChIKey searching in Google
 UniChem: a unified chemical structure cross-referencing and identifier tracking system
 Consistency of systematic chemical identifiers within and between small-molecule
databases
To find out more and to stay up-to-date
Register for updates / Read our Blog / Follow us on Twitter
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Chemical Information Bulletin Vol. 65(1) Spring 2013
- SPRESIweb version 2.12 successfully released
InfoChem is pleased to announce the successful
release of SPRESIweb 2.12.
The well-known web-based application gives
direct access to the complete content of the
SPRESI structure and reaction database that
includes now 5.52 million compounds and 4.26
million reactions, covering the literature for the
time period 1974-2011. Since 2006, all structures from the major chemical supplier catalogs were
added alongside the literature structures, thus boosting the number of molecules to the 11.8
million contained in version 2.11. Now InfoChem has given SPRESI a major refresh and resumed the
original concept of only including structures abstracted from the literature. This means that all the
small molecules and common structures from catalogs that are not included in SPRESIweb have been
removed. Therefore, SPRESI now only retains those catalog data and supplier links matching
literature structures.
In addition all the data of those chemical supplier catalogs included in SPRESIweb have been updated
and Apexmol and Ark Pharm have been added.
For more information about SPRESIweb click here or visit www.spresi.com.
- SPRESImobile App version 2.0 launched in September 2012
InfoChem is pleased to announce the successfull launch of
SPRESImobile 2.0 in September 2012. The free App, successfully
introduced on iTunes in March and developed to perform structure
and reaction searches on mobile devices, gives access to a subset
of the SPRESI reaction data (ChemReact).
Reaction searching is the most important feature of the new
iPhone and iPad App version: users are now able to perform exact,
substructure, similar and all-in-one reaction searches, editing the
queries with an ad hoc developed editor.
For more information about SPRESImobile click here.
Please feel free to contact us for more information about InfoChem, our current research projects
and our products.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Optibrium Previews Derek Nexus
for StarDrop in Hands-On
Workshop at ACS Spring National
Meeting
Toxicity of drug candidates is a major cause of expensive, late-stage failure in pre-clinical and clinical
development. At the ACS Spring 2013 National Meeting, Optibrium™ is previewing the Derek
Nexus™ module for their StarDrop™ software platform discovery. This new module provides Lhasa
Limited’s world-leading technology for knowledge-based prediction of key toxicities, integrated
within StarDrop to help guide the design and selection of high quality compounds in drug discovery.
Optibrium will introduce the new Derek Nexus module at a free lunchtime workshop “Addressing
toxicity in drug discovery.” This workshop will include a presentation by David Watson, CEO of Lhasa
Limited, introducing their Derek Nexus platform, and a hands-on opportunity to try StarDrop. The
workshop will be held on Tuesday, April 9th from 12:00 – 2:30 pm in Halls B2-C, Exhibitor Workshop
Room 1 and lunch will be provided. Places are limited, so please register at www.optibrium.com or
with the Optibrium team at booth #708 in the Exposition.
Using data from published and donated sources, Lhasa Limited’s Derek Nexus technology identifies
structure-toxicity relationships that alert users to potential causes of compound toxicity in over 40
endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.
Optibrium’s StarDrop software platform guides decisions in drug discovery to quickly identify
chemistries with a high chance of success against a drug discovery project’s objectives. StarDrop’s
unique probabilistic scoring approach to multi-parameter optimisation allows predicted and
experimental data to be given appropriate weights when balancing the many requirements for a
high quality lead or candidate compound.
The combination of these technologies will enable chemists to intuitively balance the reduction of
toxicity risk with the other requirements for a successful, safe and efficacious drug in hit-to-lead
and lead optimisation. Furthermore, the region of a compound triggering a toxicity alert will be
highlighted using StarDrop’s Glowing Molecule™ visualisation, helping to guide the interactive
redesign of compounds to reduce liabilities.
If you aren’t attending the ACS Spring meeting you can find out more about StarDrop and
Optibrium’s collaboration with Lhasa Limited at www.optibrium.com. Alternatively, call +44 1223
815 900 or email [email protected] for more information.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
TIBCO Spotfire® a Leader in Business Intelligence and Analytic Platforms
A report released by Gartner Inc. - “Magic Quadrant for Business Intelligence and Analytics
Programs” -has placed the TIBCO Spotfire® software platform in the “Leaders Quadrant”, clearly
identifying it as a market leader in business intelligence and analytics.
The report identified the TIBCO Spotfire platform as a “flexible and easy-to-use platform for… data
discovery and analysis, for authoring analytic applications, for publishing interactive and visual
dashboards, and for building predictive models and applications.” Users of the TIBCO Spotfire
software platform report “success in terms of expanded usage over the past year”, an “aboveaverage view of Spotfire's product quality” and “above-average performance scores”.
One of the greatest challenges for scientists today is the volume and diversity of data they need to
capture and analyze to make knowledgeable and informed decisions that impact both research and
business intelligence efforts. With the integration of the TIBCO Spotfire® software platform into
the Ensemble® portfolio and our Electronic Laboratory Notebook solution, scientists now have
direct access to state-of-the-art data analysis and visualization tools to reveal new insights from
their data - quickly identifying new relationships, isolating significant outliers and easily spotting
trends and patterns. More: http://www.cambridgesoft.com/news/details/?News=174.
Gartner Report Reaffirms PerkinElmer’s Leadership Position in ELN
A recently released report from technology research company Gartner has confirmed that
PerkinElmer Inc. continues to be a leader in the Electronic Laboratory Notebook (ELN) field
achieving the highest ratings of the 34 ELN vendors included in the report.
The report, ‘Manufacturers Must Consider Scientific Domain Expertise During ELN Selection’
published January 11, 2013, recognizes the critical importance of selecting an ELN vendor that can
deliver the highest levels of domain specific functionality to ensure that the solution is tightly
aligned with an organization’s scientific and business objectives. PerkinElmer's Ensemble® ELN
platform achieved the highest ratings scores of “High” or “Very High” in all six scientific and
functional domain categories (Biology, Chemistry, Formulation, Engineering, GxP and Translational
Medicine). According to the report, the “High” ratings demonstrate “an ability to deliver deep
functionality with out of the box solutions that are specific to the industry domain” while the “Very
High” scores achieved by PerkinElmer Inc. in the Chemistry and GxP domains reflect that “the
vendor has excellent scientific domain capabilities and is approaching the "de facto" standard”.
More: http://www.cambridgesoft.com/news/details/?News=173.
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Chemical Information Bulletin Vol. 65(1) Spring 2013
Thieme E-Journals – Your first choice for research and information needs
The modern, user-friendly Thieme E-Journal platform gives easy access to the complete Thieme EJournal collection, among them the chemistry-related journals SYNLETT, SYNTHESIS, SYNFACTS,
Planta Medica and Drug Research.
The Thieme E-Journal platform offers:
•
•
•
•
•
Enhanced usability and a modern interface
New features such as the image view
Enhanced search engine optimization and data delivery options for even better searching
and visibility of content (search engines, A&I services, integration with link resolvers)
RightsLink partnership for a much easier and quicker way to permissions and reprints
Compatibility for mobile devices such as tablet computers and smart phones (via mobile
browser)
Users may register for a personal account to benefit from a multitude of services including:
•
•
•
•
•
Possibility to save personal settings and queries
Customized interface
eFirst and table of contents alerting services
SDI (Selective Dissemination of Information) – alerting you to important results in your field
of interest
RSS feeds
Authors are given the possibility to publish primary chemical data together with their research
results. This service has been successfully launched for the synthetic organic chemistry journals
SYNTHESIS and SYNLETT: Analytical data from various experiments can be registered and made
available online via the Thieme E-Journal platform, using DOI recognition (Digital Object Identifiers).
This enables scientists to easily locate research articles, including accompanying data, and make
enhanced use of the scientific content.
Access the Thieme E-Journal platform:
http://www.thieme-connect.com/ejournals
Further information about primary data publication:
http://www.thieme-chemistry.com/en/products/journals/supplements/primary-data.html
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Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Officers 2013
Executive Committee
Member
Function
Tenure
Contact
Antony Williams
Chair
2013
VP Strategic Development
ChemSpider, Royal Society of Chemistry
(919) 201-1516 (voice)
Rajarshi Guha
Past Chair
2013
NIH Chemical Genomics Center,
9800 Medical Center Drive,
Rockville, MD 20852
814-404-5449 (voice)
812-856-3825 (fax)
Judith Currano
Chair-Elect
2013
Chemistry Library, University of Pennsylvania
231 S. 34th St., 5th Floor
Philadelphia, PA 19104-6323
(215) 746-5886 (voice)
(215) 898-0741 (fax)
Leah McEwen
Secretary
2012-2013
Cornell University, Clark Library
283 Clark Hall,
Ithaca, NY 14853-2501
607-255-1361 (voice)
607-255-5288 (fax)
607-229-0287 (cell)
Rob McFarland
Treasurer
2013-2014
Washington University
Campus Box 1134
1 Brookings Dr
Saint Loius, MO 63130-4862
(314) 935-4818 (voice)
(314) 935-4778 (fax)
133
Chemical Information Bulletin Vol. 65(1) Spring 2013
Bonnie Lawlor
Councilor
20132015
National Federation of Advanced Information
Services (NFAIS),
276 Upper Gulph Road,
Radnor, PA 19087-2400
215-893-1561 (voice)
215-893-1564 (fax)
Andrea TwissBrooks
Councilor
20122014
University of Chicago,
4824 S. Dorchester Avenue, Apt. 2,
Chicago, IL 60615-2034
773-702-8777 (voice)
773-702-3317 (fax)
Guenter Grethe Alternate
Councilor
2013 –
2015
352 Channing Way,
Alameda, CA 94502-7409
510-865-5152 (voice)
510-865-5152 (fax)
510-333-7526 (cell)
Charles F. Huber Alternate
Councilor
2012 –
2014
University of California, Santa Barbara, Davidson
Library
Santa Barbara, CA 93106-9010
805-893-2762 (voice)
805-893-8620 (fax)
Jeremy Garritano Program Chair
2013
Associate Professor of Library Science, Chemical
Information Specialist
Division of Physical Sciences, Engineering, and
Technology
Purdue University Libraries
(765) 496-7279 (voice)
Gregory M. Banik Membership
Chair
20122014
Bio-Rad Laboratories, Inc.
Informatics Division
Two Penn Center Plaza, Suite 800
1500 John F. Kennedy Blvd
Philadelphia, PA 19102
(267) 322-6952 (voice)
(267) 322-6953 (fax)
134
Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Officers 2013
Committee Chairs
Chair
Committee
Tenure
TBD
Audit
2013
Andrea TwissBrooks
Awards
20122014
University of Chicago,
4824 S. Dorchester Avenue, Apt. 2,
Chicago, IL 60615-2034
773-702-8777 (voice)
773-702-3317 (fax)
TBD
Careers
David
Martinsen
Communications and
Publications
20132015
American Chemical Society
1155 16th St NW
Washington, DC 20036
(202) 452-2110 (voice)
Susanne
Redalje
Constitution, Bylaws, and
Procedures
2007-
University of Washington, Chemistry Library
Rm. 163 Suzallo-Allen Library
BOX 351700
Seattle, WA 98195-2900
206-543-2070 (voice)
Grace Baysinger Education
20132015
Head Librarian, Stanford University
Swain Chem & Chem Eng Library
MC 5081
364 Lomita Dr.
Stanford, CA 94305-5006
(650) 725-1039 (voice)
(650) 725-2774 (fax)
Rob McFarland Finance
20132014
Washington University
Campus Box 1134
1 Brookings Dr
Saint Loius, MO 63130-4862
(314) 935-4818 (voice)
(314) 935-4778 (fax)
Rajarshi Guha
2013
NIH Chemical Genomics Center,
9800 Medical Center Drive,
Rockville, MD 20852
814-404-5449 (voice)
812-856-3825 (fax)
Fundraising
135
Contact
Chemical Information Bulletin Vol. 65(1) Spring 2013
Gregory M.
Banik
Membership
20122014
Bio-Rad Laboratories, Inc.
Informatics Division
Two Penn Center Plaza, Suite 800
1500 John F. Kennedy Blvd
Philadelphia, PA 19102
(267) 322-6952 (voice)
(267) 322-6953 (fax)
Rajarshi Guha
Nominating
2013
NIH Chemical Genomics Center,
9800 Medical Center Drive,
Rockville, MD 20852
814-404-5449 (voice)
812-856-3825 (fax)
Jeremy
Garritano
Program
2013
Associate Professor of Library Science,
Chemical Information Specialist
Division of Physical Sciences, Engineering,
and Technology
Purdue University Libraries
(765) 496-7279 (voice)
136
Chemical Information Bulletin Vol. 65(1) Spring 2013
CINF Officers 2013
Divisional Representatives and Liaisons
Representative Division
Tenure Contact
Susan K.
Cardinal
2006- University of Rochester, Carlson
Library
Box 270236,
Rochester, NY 14627
585-275-9007 (voice)
585-273-4656 (fax)
SLA DCHE
Guenter Grethe ACS Multidisciplinary Program
Planning Group
2007- 352 Channing Way,
Alameda, CA 94502-7409
510-865-5152 (voice)
510-865-5152 (fax)
510-333-7526 (cell)
Guenter Grethe Biotechnology Secretariat
2002- 352 Channing Way,
Alameda, CA 94502-7409
510-865-5152 (voice)
510-865-5152 (fax)
510-333-7526 (cell)
Erja Kajosalo
ASIS&T STI
2006- Massachusetts Institute of
Technology, MIT Libraries 14S-134
77 Massachusetts Ave.,
Cambridge, MA 02139-4307
Seattle, WA 98195
617-253-9795 (voice)
617-253-6365 (fax)
781-223-3869 (cell))
Peter F. Rusch
ACS Committee on Nomenclature,
Terminology, and Symbols
2006- Rusch Consulting Group,
162 Holland Court,
Mountain View, CA 94040-3864
650-961-8120 (voice)
650-961-8120 (fax)
Mitchell C.
Brown
ACRL STS
2009
137
University of California at Irvine,
Irvine, CA 92697-8200
949-824-9732 (voice)
949-824-3114 (fax)
Chemical Information Bulletin Vol. 65(1) Spring 2013
Other Functionaries
Member
Function
Tenure
Contact
Bonnie Lawlor Archivist/Historian 2006-
National Federation of Advanced Information Services
(NFAIS),
276 Upper Gulph Road,
Radnor, PA 19087-2400
215-893-1561 (voice)
215-893-1564 (fax)
Danielle
Dennie
Concordia University, Vanier Library Building
7141 Sherbrooke St. W.,
Montréal (QC), H4B 1R6, Canada
514.848.2424 x 5237 (voice)
Webmaster
20112013
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