Fast and accurate prediction of protein side-chain conformations

Shide Liang; Dandan Zheng; Chi Zhang; Daron M. Standley

doi:10.1093/bioinformatics/btr482

Fast and accurate prediction of protein side-chain conformations

Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley

Research output: Contribution to journal › Comment/debate › peer-review

38 Scopus citations

Abstract

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 errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.

Original language	English (US)
Article number	btr482
Pages (from-to)	2913-2914
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	20
DOIs	https://doi.org/10.1093/bioinformatics/btr482
State	Published - Oct 2011

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr482

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title = "Fast and accurate prediction of protein side-chain conformations",

abstract = "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 errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.",

author = "Shide Liang and Dandan Zheng and Chi Zhang and Standley, {Daron M.}",

note = "Funding Information: Funding: DMS was supported by the Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST), Japan Science for the Promotion of Science (JSPS).",

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AU - Liang, Shide

AU - Zheng, Dandan

AU - Zhang, Chi

AU - Standley, Daron M.

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N2 - 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 errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.

AB - 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 errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement.

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Fast and accurate prediction of protein side-chain conformations

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