Fast and accurate prediction of protein side-chain conformations.
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ABSTRACT: Summary
We developed a fast and accurate side-chain modeling program [Optimized Side Chain Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid rotamer model. The average computing time was 18 s per protein for 218 test proteins with higher prediction accuracy (1.1% increase for ?(1) and 0.8% increase for ?(1+2)) than the best performing program developed by other groups. We show that the energy functions, which were calibrated to tolerate the discrete errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.Availability
OSCAR-star and the 218 test proteins are available for download at http://sysimm.ifrec.osaka-u.ac.jp/OSCAR CONTACT: standley@ifrec.osaka-u.ac.jpSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Liang S
PROVIDER: S-EPMC3187653 | biostudies-literature | 2011 Oct
REPOSITORIES: biostudies-literature
Publications
Fast and accurate prediction of protein side-chain conformations.
Liang Shide S Zheng Dandan D Zhang Chi C Standley Daron M DM
Bioinformatics (Oxford, England) 20110827 20
<h4>Summary</h4>We developed a fast and accurate side-chain modeling program [Optimized Side Chain Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid rotamer model. The average computing time was 18 s per protein for 218 test proteins with higher prediction accuracy (1.1% increase for χ(1) and 0.8% increase for χ(1+2)) than the best performing program developed by other groups. We show that the energy functions, which were calibrated to tolerate the discrete ...[more]
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