Rosetta
Steven Bitner
Objectives
Introduction
 How Rosetta works
 How to get it
 How to install/use it
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Introduction
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Developed in the David Baker lab at University of Washington
Winner of CASP (Critical Assessment of Structure Prediction)
competition at Lawrence Livermore Labs, CA
 Implies that Rosetta is the best de novo predictor
Rosetta is a protein prediction and docking software package
Also used to design proteins from (nearly) arbitrary 3-D shapes
 November, 2003, ‘Top-7’ first synthetic protein
Rosetta home
 Human Proteome Folding Project
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Also called the World Community Grid
TOP-7 protein designed, or
synthesized, using Rosetta
How Rosetta Works
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Minimize energy in the folded state
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Side-chains simplified to a centroid located at center of
mass of the side-chain
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Uses a combination of energy formulas based on the likelihood
of particular structures, and the fitness of the sequence
Average of observed side-chain centroids in known structures
Local sequence does not decide the local structure, it
only biases the decision
Non-local favorable conditions
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Buried hydrophobic fragments
Paired β strands
Specific side-chain interactions
How Rosetta Works (Energy
functions)
How Rosetta Works (Energy
functions) cont.
How Rosetta Works cont.
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Side-chains are added using Monte Carlo
methods
Overlaps of side-chain centroids and backbone
atoms are penalized
Uses probabilistic β-strand pairing and β-sheet
patterns
Fragment Insertion - more later
Fragment Assembly - more later
Fragment Insertion
Finds three and nine residue fragments
from known library and replaces unknown
torsion angles with the ‘known’ ones
 Scores all windows of three and nine
residues
 Create fragment list with the 200 best
three residue and 200 best nine residue
fragments
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Fragment Assembly
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Randomly choose a nine residue fragment from
the top 25 fragments in the ranked list
 Score
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this replacement, negatives are kept
Each simulation chooses a different random
start and attempts 28,000 nine residue
insertions
Next 8,000 attempted three residue insertions
are scored with the overall structure
Why it’s Fast
Changes multiple angles simultaneously
by using fragments from the library
 Angular changes are discrete, not
continuous
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Getting the Software
Go to the website (bakerlab.org)
 Register by clicking on Rosetta Licensing
Information
 Go to link in email that is sent to you
 Download
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Installing software
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Upload onto a Linux machine, or other
supported platform
(see README_platform)
 UTD’s Apache
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server does not work
Unpack using tar –zxvf ‘filename’
Go into rosetta++ directory
Make gcc
 Takes
about 20 minutes
 This is the standard version
Different install versions
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Other ways to install than make gcc
 See
the README in rosetta++ directory
 GCCDEBUG – for use if you plan on
making updates to the software
Using the downloaded software
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PDB file must be in the same directory as
the program or the paths.txt file must be
updated
 paths.txt
must be updated for the data source
the default is a non-existant directory
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User guide – assumes a good knowledge
of the system
Using Rosetta
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Rosetta on-line Server – 200 residues at a
time
http://rosettadesign.med.unc.edu/index.html
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Robetta site – down until mid October ’06
http://robetta.bakerlab.org/
Downloaded software
 Can use res files to specify portions of the
backbone, or you can select the residues
that you wish to pack on the web server
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Interpreting results
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Output file fields
 Rosetta
Commons site also has similar
document except the energy labels use E for
energy in stead of LJ and LK for LennardJones and Lazaridis-Karplus respectively as
the prefix
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E.g. Lennard-Jones attractive score is Eatr in the
Rosetta commons output file and LJatr in the
Rosetta Design output file
Input PDB file 1HOE–
displayed using PyMol
Output PDB file 1HOE – displayed
using PyMol
1ubq
Before
→
After
Software used for this presentation
Rosetta – release 2.1.0
 Rosetta Design Server
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http://rosettadesign.med.unc.edu/index.html
PyMol for visualization
RCSB PDB
http://www.rcsb.org/pdb/Welcome.do
References
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Rosetta Design Web Server
http://rosettadesign.med.unc.edu/documentation.html
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Protein Structure Prediction Using Rosetta, Numerical
Computer Methods, C.A. Rohl, C.E. Strauss, K.M.
Misura, D. Baker, pp. 66-93, 2004
README documentation included with rosetta2.0.1
Rosetta Website https://www.rosettacommons.org/
David Baker Lab Homepage http://www.bakerlab.org/