rosetta steven bitner. objectives introduction how rosetta works how to get it how to install/use it
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RosettaSteven Bitner
Objectives
Introduction How Rosetta works How to get it How to install/use it
Introduction
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 Also called the World Community Grid
TOP-7 protein designed, or synthesized, using Rosetta
How Rosetta Works
Minimize energy in the folded state Uses a combination of energy formulas based on the likelihood
of particular structures, and the fitness of the sequence Side-chains simplified to a centroid located at center of
mass of the side-chain 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 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.
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
Fragment Assembly
Randomly choose a nine residue fragment from the top 25 fragments in the ranked list Score 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
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
Installing software
Upload onto a Linux machine, or other supported platform
(see README_platform) UTD’s Apache 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
Other ways to install than make gccSee the README in rosetta++ directoryGCCDEBUG – for use if you plan on
making updates to the software
Using the downloaded software
PDB file must be in the same directory as the program or the paths.txt file must be updatedpaths.txt must be updated for the data source
the default is a non-existant directory User guide – assumes a good knowledge
of the system
Using Rosetta
Rosetta on-line Server – 200 residues at a time http://rosettadesign.med.unc.edu/index.html
Robetta site – down until mid October ’06http://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
Interpreting results
Output file fieldsRosetta Commons site also has similar
document except the energy labels use E for energy in stead of LJ and LK for Lennard-Jones and Lazaridis-Karplus respectively as the prefix
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
1 u b q
Before → After
Software used for this presentation
Rosetta – release 2.1.0 Rosetta Design Server
http://rosettadesign.med.unc.edu/index.html PyMol for visualization RCSB PDB
http://www.rcsb.org/pdb/Welcome.do
References
Rosetta Design Web Server http://rosettadesign.med.unc.edu/documentation.html
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/
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