ChemBioOffice 2008
Daniel Oberlin
Director, Software Development
ChemBioOffice 2008
The Desktop Productivity Suite for Scientists
ChemBioOffice
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The industry-standard desktop suite for chemists and biologists
Interoperates with and complements Microsoft Office
Integration with CambridgeSoft Enterprise Solutions
A vital productivity tool any organization
ChemBioOffice 2008
The Desktop Productivity Suite for Scientists
ChemDraw Excellence
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Structure diagram generation
– Rigorously conforms to the IUPAC conventions
– Licensed commercially to other vendors
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Structure rendering
– Highest quality – the details set us apart
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Name to Structure
– More names, best accuracy
– Error detection and correction
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Chemical data formats
– More formats, best accuracy
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Ease of use
– Most intuitive, most efficient
ChemDraw for Analysis
H
OH
HO
H
(S)
H
(R)
(S)
(R)
(R)
H
HO
6
5
4
OH
O
HO
3
PPM
H
2
1
0
ChemBioDraw 11.0
New features and improvements
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New Chemistry Features
– Sequence tool
– Structure clean-up and stereochemistry enhancements
– New reaction interpretation, SD file support, R-Group logic
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Improved productivity and application integration
– Customizable themes and preferences
– Hotlink to Databases, Chem3D Hotlink
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New drawing features
– Flexible arrows
– Freehand pen tool
– Integrated BioDraw including new plasmid map
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Extended platform support
– Windows Vista
– MSOffice 2007
– Native support of Intel on Mac
Work faster with ChemDraw
ChemDraw Reduces Drawing Time
Customizable
Hotkeys
Hotkey
Result
1
Change to single bond.
2
Change to double bond.
3
Change to triple bond.
4
Change to quadruple bond.
c
Center a double bond.
l
Position a double bond to the left.
f
Bring a bond to the front.
a
A
A or 5
Ac
b
Br
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Use Hotkeys to draw chemical
structures in less than half the time
Avoid going back to the Tools Palette
to change tools - those mouse
motions and clicks add up to a lot of
extra time!
Share Hotkey customizations with
colleagues
Work faster with ChemDraw
ChemDraw Reduces Drawing Time
Customizable
Templates
Complex structures take
seconds to draw vs.
minutes
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Save hours by using predefined rings,
templates and drawings
Create custom templates, reducing
time for repeated experiments
Reduce Document Clutter
Communicate chemistry more effectively
Customizable
Nicknames
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Simplify and speed up chemical drawings using Nicknames
Draw structures where parts of the molecule aren’t shown in full
detail, but instead are represented by a chemically intelligent label
that can be expanded and contracted
Define new nicknames in ChemDraw to fit your research
Reduce Document Clutter
Communicate chemistry more effectively
Customizable
Nicknames
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Simplify and speed up chemical drawings using Nicknames
Draw structures where parts of the molecule aren’t shown in full detail,
but instead are represented by a chemically intelligent label that can
be expanded and contracted
Define new nicknames in ChemDraw to fit your research
Reduce Document Clutter
Communicate chemistry more effectively
Customizable
Nicknames
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Simplify and speed up chemical drawings using Nicknames
Draw structures where parts of the molecule aren’t shown in full detail,
but instead are represented by a chemically intelligent label that can
be expanded and contracted
Define new nicknames in ChemDraw to fit your research
New Sequence tool
Easily Create Amino Acid, DNA, RNA sequences
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Draw peptide and nucleotide
sequences
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Several modes:
- Single-letter amino acid tool
- Three-letter amino acid tool
- DNA tool
H
N
- RNA tool
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Termini are labeled
depending on the type of
sequence drawn
Expand and contract single or
multiple labels and
sequences
O
O
H
N
OH
N
H
N
H
H
•
OH
HS
O
O
A
C
G
T
Highest Presentation Quality Graphics
Instant Structure and Reaction Clean-up
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One click with Structure or Reaction Cleanup provides neater,
more accurate drawings
Compare to multiple undo’s and adjustments to the structure –
significant time savings
Fixed Lengths and Fixed Angles options
Major Improvements to algorithm in version 11 supports a wide
spectrum of structure types
Removal of overlap: Bridged rings
H
HH
O
O
S
S
O
S
O
Selection of base
ring in cyclic system
O
S
H
H
H
O
O
Positioning of
hashed and
wedged
bonds
Vertically
oriented
carbonyls
Advanced Drawing Conventions
Stereochemistry enhancements
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ChemDraw 11 has been enhanced to recognize the common drawing styles
that represent tetrahedral stereochemistry without using stereo bonds in
their usual sense
Changes are consistent with the latest IUPAC recommendations for the
depiction of stereochemistry
Examples:
HO
R
O
HO S
R
OH
R
R
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CHO
OH
(R)
HO
R
S
HO
O
OH
S
R
S
OH
OH
OH
H
HO
H
H
R
S
R
R
OH
H
OH
OH
CH2OH
OH
OH
Change ChemDraw, not your Workflow
Customizable Themes and Preferences
ISIS/Draw compatibility mode in ChemDraw
ChemDraw
ISIS Compatibility
ISIS/Draw Compatibility
Use ChemDraw in place of ISIS Draw
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ISISTM R-group Query Compatibility
– Query a structure database using R-Groups and logical conditions
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SD File Support
– Import an SD file with multiple structures into ChemDraw 11.0
– ChemDraw will display all of the structures in one drawing
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Full MDL File Format Compatibility
– Reading, writing of SKC, TGF, MOL, MOL V3000 & RXN files
– Support for many other file formats for transfer of structures to other
applications and creating presentation quality graphics
– Support for Data S-Groups – attach data to objects
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Full Compliment of Query features
– Alternative groups, element lists, variable attachments, and more…
Chem3D Hotlink
Integrated structural visualization
• A separate floating window shows a 3D model of the current structure
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Chem3D must be also be installed
Database Gateway Livelink
Search structural databases in real time
• Real-time search
– Search as you draw
– Search all CS databases
– Search internal databases
• Drill-down results
– Click on data source name to see
results from that source
– Links are opened in an external browser
window so work in ChemDraw can
continue…
ChemDraw NMR Prediction
Helps confirm Chemical Structures
• 1H NMR includes splitting Patterns
• Calculate predicted 13C NMR spectrum
ChemDraw NMR Prediction
Helps confirm Chemical Structures
• 1H NMR includes splitting Patterns
• Calculate predicted 13C NMR spectrum
6
5
4
3
PPM
2
1
0
MestReC Std processes 1D NMR Spectra
Chemists can analyze their results in seconds
Phase
Correction
MestReC Lite Import File Formats
Data Format
Vendor
Dimensions
VXR/Unity/Inova
Varian
1D **
Gemini/VXR
Varian
1D
XWINNMR/UXNNMR
Bruker
1D **
Aspect
2000/3000
Bruker
1D
Win-NMR
Bruker
1D
JEOL GX/EX
JEOL
1D
CDFF Nuts
AcomNMR
1D **
JCAMP-DX 5.0
IUPAC
1D
NTNMr
Tecmag
1D
SwaN-MR
Menarini
1D
SIEMENS NMR
Siemens
1D
SIEMENS NMR
Nicolet/GE
1D
** Full version of MestReC also reads 2D in this format
Baseline
Correction
Analysis
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Basic NMR processing and
analysis - ideal for multiple
chemists running large
numbers of routine
experiments
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Compliments ChemDraw’s
NMR prediction capabilities
Instantly Generate Structures from Names
Do more Lab work, less Drawing
Lambda
convention
Isotopes
N
Inner salts
NH
Porphyrin
s
HN
N
porphyrin
Name-to-Struct now handles more structure types and
has a typo recognition feature
Highest Presentation Quality Graphics
Intuitive Freehand sketching tool
• The toolbar contains two items, “Draw Curve” (default) and
“Edit Curve”
• Holding the “Shift” key reduces the amount of smoothness
• The curves created can be further modified by selecting
and dragging control points
Highest Presentation Quality Graphics
Adjustable Shapes, Arrows and more
• Arrow Types include: No-go,
unbalanced equilibrium, dipole,
multiple arrowheads
• Adjustable Arrows: Full control
over arrow properties including
Curves, color fill and shading illustrate complex
chemistry/biology mechanisms
• Rotatable and adjustable
geometric shapes – rectangles
and ovals
SH
SH
O
H3C
CH3
CH3
2,7,9-trimethyl-4aH -xanthene-4,5-dithiol
• Color-faded geometric shapes –
rectangles and ovals
SH
SH
O
H3C
CH3
H3C
BioDraw
Illustration of Biological and Biochemical Systems
ANTIGEN PRESENTING CELL
Cytoplasm
SIGNAL 1
Extracellular
RAS
RAF
CD3
cd 42
Cytoplasm
PAK
MEK
MEKK
ERK 1,2
SEK
ELK-1
JNK
ELK-1 Activates
c-f os transcription
c-Fos
Interlukin 2
enhancer
c-Fos
c-Jun
AP-1 transcription factor
c-Jun
Nucleus
Integrate Chemistry and Biology Drawings
Facilitate Communication between Scientists
BioDraw allows the illustration of…
– Biological pathways
– Cell macro-structures
– Plasmid maps
… which may be combined with
chemical structures, reactions, and other
content from ChemDraw…
Integrate Chemistry and Biology Drawings
Facilitate Communication between Scientists
Draw Biological Pathways
One or Two-substrate enzyme
Receptor
Ion Channel
Helix Protein
Linear membrane
Arc membrane
Golgi body
Cloud
G-Protein (alpha, beta or gamma subunit)
Immunoglobin
DNA
Micelle
Ellipse membrane
Endoplasmic Reticulum
Mitochondrion
BioDraw - New Drawing tools
Enhanced illustration of biological processes
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New tRNA Tool
New Ribosome Tool
New Plasmid Maps
DNA helix strands can
now be selected
individually for
modification
• Protein helix strands
and cylinders can now
be individually selected
and modified
Integrate Chemistry and Biology Drawings
Facilitate Communication between Scientists
• BioDraw features are fully
integrated into ChemBioDraw Ultra
• Use any BioDraw tool in
any ChemDraw document
Annotations
Add information to Objects in ChemBioDraw
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The Annotation Tool allows the user to add information to objects. The information will
be stored and show as a keyword and content
– Keyword: will describe the type of information
– Content: will contain the information.
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A list of keywords has been pre-defined (Description, Name, Other Info, and Type)
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The user also has the option to add new keywords
ChemBio3D 11
Bio3D is for…
• Medicinal Chemists…
– Comparing structures and properties of
trial compounds
– Visualizing small molecules in a protein
active site
– Building new trial compounds
• Biochemists…
– Viewing and customizing the display of
protein systems
– Showing details of active site regions
Chem3D is for…
• All Chemists…
– Easily generating realistic 3D structures
using ChemDraw
– Understanding molecular flexibility and
motion using simulation
– Creating high resolution images of
chemical systems for publication
– Embedding live, interactive models in web
pages and PowerPoint
Both Come with ChemBio3D
Chem3D
ChemBio3D
Ultra
Bio3D
ChemBio3D 11 New Features
• Medicinal Chemistry Structure Browser
– Compare structures and properties
• MMFF94 Force Field Minimization
– More atom types and better parameters
• Improvements to the Model Explorer
– Drag-and-drop, improved performance
• And many other improvements…
Structure Browser
New for ChemBio3D 11
Quality visualization on the Desktop
Structural insights, Team collaboration
ChemBio3D Ultra
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Medicinal and cheminformatics
groups can access high quality,
easy to use visualization and
computation tools at a low cost
Visualize results from
Computational Chemistry
Group - assist in designing the
next round of synthetic targets
Protein and Nucleic Acid
Ribbon Diagrams provide
insight into tertiary and
quaternary structure of proteins
and protein complexes
ChemBio3D Ultra: ChemDraw Panel
Build models quickly using ChemDraw
• Easily draw 3D structures using embedded ChemDraw window
• Always in-sync with 3D view
• Time saving benefits of ChemDraw available within Chem3D!
Model Explorer Tree Control
Efficiently explore the structure of large molecules
Chem3D Visualization
More Visualization and Display Options
Kekule / Delocalized Display Mode
• Toggle between dashed line and
alternating single-double bond
representation of delocalized and aromatic
bonds.
Atom Properties
• New Atom Property Table in v11
• Color-code your model based on
virtually any property
• Partial Charges from QM
Calculations and Force field atom
types and charges treated as
atom properties
MMFF94 Force Field Minimization
Support for Protein Calculations
• Specifically designed to perform energy calculations and
minimizations on proteins and other biological structures
• More atom types and better parameters…
• MMFF94 was parameterized as a combined
organic/protein force field…
• MMFF94 is equally applicable for proteins, small molecules, or systems
containing both.
• The MMFF94 force field provides a richer set of atom types, so
MMFF94 calculations may succeed in cases where MM2 calculations
fail due to missing atom types.
ChemFinder
Chemical Database Management System
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View and Build Your Own Chemical Databases
Create your own forms
Store chemical structures, properties, notes and tables of data
Integrated with ChemDraw
Search data by
– Chemical structure (including sub-structure)
– Wild card text searches
– Numeric range searches
ChemFinder
Chemical Database Management System
Title bar
Main toolbar
Record
toolbar
Search toolbar
Main
menu
Text toolbar
Main
form
Form
toolbar
Framed
data box
Structure
box
Subform
Shortcut
menu
Table
header
Data
table
Status
bar
Read-only Add
indicator
indicator
Query
indicator
Current
record
Current
list size
To tal
database size
Get more out of your data
Analysis right in ChemFinder with
BioViz
BioViz
Data
visualization
and analysis
right in
ChemFinder
No need to
switch back and
forth to other
apps
Analyses are
saved with the
form
Get more out of your data
Lots of options with BioViz
BioViz
Data visualization
Plot any numeric values
Flexible plot styles and display
Filter plot by any numeric criteria
Color plots by hitlist
Synchronization between plots
Data analysis
Statistics, regressions
List manipulation
Mouse over points to show details
Get more out of your data
Chemically Intelligent Plots
R-Group tables and R-Group analysis
• Integrated with
BioViz
• Sortable by Rgroup
• Plot according to
substituent
membership
Get more out of your data
Subform data at a glance
Subform plots
• You can create a variety of subforms with ChemFinder including
miniature plots inside
subform boxes which
plot one or two
columns of numeric
data from the set of
records showing in
the subform.
Compound Profiles
Compare structures based on Properties
Compound profiles
Visually compare and rank structures based on values of selected
properties and the cost profile associated with each property.
ChemFinder 11 Programming Options
Python, ChemScript and CAL
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Programming with Python
- Python scripts can be attached to form buttons or trigger events,
can be developed and debugged in the enhanced Script Editor -now featuring interactive line-by-line execution -- and output can be
displayed in a new dockable text window
Integrated with ChemScript
Chemical Intelligence within Excel
Chemical calculations on Multiple Structures
ChemDraw/Excel
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Add chemical structures and other data from
ChemDraw, MDL SDFiles or a ChemFinder
database to an Excel spreadsheet
Convert Names or SMILES Strings to Structures
Search using the same search features as
ChemFinder
Perform calculations on chemical structures
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ISSTRUCTURE
ISREACTION
CHEM.FORMULA
CHEM.MOLWEIGHT
CHEM.NUM.HBAACCEPTORS
CHEM.NUM.HBDONORS
CHEM.SMILES
CHEM.COMPOSITION
CHEM.NUM.ATOMS
Property
Function
LogP
Molar Refractivity
Henry’s Law Constant
Boiling Point
Freezing Temperature
Critical Temperature
Critical Pressure
Critical Volume
Heat of Formation
Gibbs Free Energy
Ideal Gas Thermal Capacity
tPSA
CHEMPROP.LOGP
CHEMPROP.MR
CHEMPROP.HENRY.LAW.CONSTANT
CHEMPROP.BOILING
CHEMPROP.FREEZING
CHEMPROP.CRITICAL.TEMP
CHEMPROP.CRITICAL.PRESSURE
CHEMPROP.CRITICAL.VOLUME
CHEMPROP.HOF
CHEMROP.GIBBS
CHEMPROP.IDEAL.GAS
CHEMPROP.TPSA
Combinatorial Chemistry within Excel
Automatic Generation of Product Lists
CombiChem/Excel
• Enter a reaction with generic reactants & products with R-groups and
reagents reagent lists
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CombiChem/Excel generates the resulting product list – no need to
draw the resulting structures by hand
• Use Excel and ChemDraw/Excel tools to generate properties for the
products and manipulate the data, such as re-ordering of products
based on properties such as molecular weight
• Prior Limits on the number of products lifted in newer versions, with
option to enumerate into a ChemFinder database (no limit)
New Workgroup solutions
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To date CambridgeSoft offered Desktop or Enterprise solutions.
– Desktop solutions are adequate for individual users
– Enterprise solutions require Oracle and many days of services and
customization. Fits large organizations.
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There was no offering for small groups that work collaboratively but do
not have the resources to deploy a fully fledged enterprise solutions.
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New offerings:
– ChemBioOffice Workgroup Ultra 2008
– ChemBioOffice Workgroup Pro 2008
ChemBioOffice: offering the right solution
ENotebook, Inventory & BioAssay
Desktop
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SQL Server 2005 Express - self tuning RDBMS
Support multiple users
Supports Vista
1-10 users
Database limit now doubled - 4GB
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For example: Inventory with 1000 compds + 1000 containers +
1000 MSDS 0.1 MB pdfs = 140 MB
ENotebook, Inventory & BioAssay
Workgroup
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Parallel Desktop and Workgroup products
SQL Server 2005
Easy upgrade from Desktop to Workgroup
No limit on the Database size
10-100 users
Better performance, particularly with many users
E-notebook Workgroup
Eliminate hours writing & searching lab results
• Basic features of ELN:
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Audit Trails, AutoText, Stoichiometry Calculations,
Configurability, Document Pages, Extensive Data Types,
Galactic spectra
• Share database - support multiple users
• SQL Authentication
• Uses ChemDraw 11
E-notebook Workgroup
Eliminate hours writing & searching lab results
Collection
Tree
Sections
Stoichiometry
Grid
Reaction
Reaction
Conditions
Audit Trail
AutoText
Inventory Workgroup
Workgroup Chemical Inventory Management
• SQL Server Role-based Security
• Cascading Location Model
• Audit Trail - logs all changes relating to
Locations, Containers, and Substances
• EHS, Reporting, Barcode Labels,
• Suppliers/MSDS through integrated
ChemACX.com
• Load your own MSDS, enter your own EHS
data, create reports with it.
• Utility to import Excel data
• Structure intelligence using MolServer – can be
deployed on the DB server
• Integration with ChemACX.Com
• Reconcile Location Contents
Inventory Workgroup
Chemical Inventory Management
• Save money: know which chemicals you have, and where they are
• Produce
customized reports
– OSHA compliance
– Controlled
substances
– Out of Date Stock
– EHS Reporting
– Barcode Labels
BioAssay Workgroup
Storage and analysis for biological data
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Flexible Assay
Definition model
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Multi-user access
Role level
permissions
Graphing
Enhancements
Report Engine
BioAssay, ENotebook & Inventory
Workgroup Services Options
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On-site Support Services:
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Migration Desktop Æ Workgroup (SQL Server):
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Migration SQL Æ Enterprise (Oracle):
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Database schemas are similar; 3-15 days
Installation/Configuration Services:
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0-3 days of Support/Service Recommended
1-3 Days On-site Assistance Recommended
Training Services:
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E-Notebook, Inventory, BioAssay Administrator, User Training Available
Training Courses are also available for ChemBioViz Desktop applications
BioAssay, ENotebook & Inventory
Workgroup ASL
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Annual Site License
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Unlimited usage within institution (hence lower cost per user)
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All departments have access to the specific software they need
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Software updates and administrator support included
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Software can be used on any machine (lab, laptop, home use)
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Site licenses reduce support load
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Multi-year site licenses reduce long-term cost
ChemBioOffice Annual Site License
Cost Effective Collaboration
• Unlimited usage within organization
– lower cost per user
• All departments have access to the software
• Updates and administrator support included
• Software can be used on any machine
– lab, laptop, or home use
• Site licenses reduce support load
– Individual online software download
• Multi-year site licenses reduce long-term cost
Conclusion
• Thank you for your time!