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Welcome to RosettaBackrub

This is the flexible backbone protein structure modeling and design server of the Kortemme Lab. The server utilizes the "backrub" method, first described by Davis et al.1, for flexible protein backbone modeling implemented in Rosetta2,3,5,6,7.

The server input is a protein structure (a single protein or a protein-protein complex) in PDB format uploaded by the user or obtained directly from the PDB plus some application-specific parameters. The server output is dependent on the application:

  • Point mutation5: generates modeled structures and Rosetta scores for single and multiple point mutants in monomeric proteins;
  • Backbone ensemble2: creates near-native structural ensembles of protein backbone conformations (for monomeric proteins) and sequences consistent with those ensembles;
  • Sequence tolerance6,7,3: predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity.

For a tutorial on how to submit a job and interpret the results see the documentation and the references below. Please also check for current announcements.

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For questions, please read our documentation, see the references below, or contact support.

[1] Davis IW, Arendall III WB, Richardson DC, Richardson JS. The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances.
Structure, Volume 14, Issue 2, 2nd February 2006, Pages 265-274

[2] Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. A Correspondence between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family.
PLoS Computational Biology, May 2009

[3] Humphris EL, Kortemme T. Prediction of Protein-Protein Interface Sequence Diversity using Flexible Backbone Computational Protein Design.
Structure, Volume 16, Issue 12, 12th December 2008, Pages 1777-1788

[4] Lauck F, Smith CA, Friedland GD, Humphris EL, Kortemme T. RosettaBackrub - A web server for flexible backbone protein structure modeling and design.
Nucleic Acids Research, Volume 38, Issue suppl. 2, Pages W569-W575

[5] Smith CA, Kortemme T. Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction.
Journal of Molecular Biology, Volume 380, Issue 4, 18th July 2008, Pages 742-756

[6] Smith CA, Kortemme T. Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains.
Journal of Molecular Biology, Volume 402, Issue 2, 17th September 2010, Pages 460-474

[7] Smith CA, Kortemme T. Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using Rosetta Backrub Flexible Backbone Design.
PLoS ONE 6(7): e20451. doi:10.1371/journal.pone.0020451

   
"RosettaBackrub" is available for NON-COMMERCIAL USE ONLY at this time. [ Terms of Service ]
Copyright © 2009 Tanja Kortemme, Florian Lauck and the Regents of the University of California San Francisco
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