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Nucleic Acids Res. 2010 Jul;38(Web Server issue):W569-75. doi: 10.1093/nar/gkq369. Epub 2010 May 12.

RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

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  • 1Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.

Abstract

The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein-protein interfaces. The three protocols have been validated on experimental data. Starting from a user-provided single input protein structure in PDB format, the server generates near-native conformational ensembles. The predicted conformations and sequences can be used for different applications, such as to guide mutagenesis experiments, for ensemble-docking approaches or to generate sequence libraries for protein design.

PMID:
20462859
[PubMed - indexed for MEDLINE]
PMCID:
PMC2896185
Free PMC Article

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