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

Lauck, F.; Smith, C. A.; Friedland, G. F.; Humphris, E. L.; Kortemme, T.

doi:10.1093/nar/gkq369

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

Journal Article · Wed May 12 00:00:00 EDT 2010 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkq369· OSTI ID:1625480

Lauck, F. ^[1]; Smith, C. A. ^[2]; Friedland, G. F. ^[3]; Humphris, E. L. ^[4]; Kortemme, T. ^[2]

Univ. of California, San Francisco, CA (United States). Dept. of Bioengineering and Therapeutic Sciences; DOE/OSTI
Univ. of California, San Francisco, CA (United States). Dept. of Bioengineering and Therapeutic Sciences
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States). Technology Division; Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States). Biomass Science and Conversion Technology Dept.
Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry

The Rosetta-Backrub 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.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: NA0003525

OSTI ID:: 1625480

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 38; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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