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


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.

SUBMITTER: Lauck F 

PROVIDER: S-EPMC2896185 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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

Lauck Florian F   Smith Colin A CA   Friedland Gregory F GF   Humphris Elisabeth L EL   Kortemme Tanja T  

Nucleic acids research 20100512 Web Server issue


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  ...[more]

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