Fast and accurate prediction of protein side-chain conformations

被引：46

作者：

Liang, Shide ^{[1
]}

Zheng, Dandan ^{[2
]}

Zhang, Chi ^{[3
]}

Standley, Daron M. ^{[1
]}

机构：

[1] Osaka Univ, Immunol Frontier Res Ctr, Syst Immunol Lab, Suita, Osaka 5650871, Japan

[2] Virginia Commonwealth Univ, Massey Canc Ctr, Dept Radiat Oncol, Richmond, VA 23298 USA

[3] Univ Nebraska, Sch Biol Sci, Ctr Plant Sci & Innovat, Lincoln, NE 68588 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 20期

关键词：

D O I：

10.1093/bioinformatics/btr482

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 chi(1) and 0.8% increase for chi(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.

引用

页码：2913 / 2914

页数：2

共 10 条

[1] Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation [J].

Cao, Yang ;

Song, Lin ;

Miao, Zhichao ;

Hu, Yun ;

Tian, Liqing ;

Jiang, Taijiao .

BIOINFORMATICS, 2011, 27 (06) :785-790

[2] Probing the role of packing specificity in protein design [J].

Dahiyat, BI ;

Mayo, SL .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (19) :10172-10177

[3] Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model [J].

de Bakker, PIW ;

DePristo, MA ;

Burke, DF ;

Blundell, TL .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 51 (01) :21-40

[4] Improved prediction of protein side-chain conformations with SCWRL4 [J].

Krivov, Georgii G. ;

Shapovalov, Maxim V. ;

Dunbrack, Roland L., Jr. .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 (04) :778-795

[5] Side-chain modeling with an optimized scoring function [J].

Liang, SD ;

Grishin, NV .

PROTEIN SCIENCE, 2002, 11 (02) :322-331

[6] Protein loop selection using orientation-dependent force fields derived by parameter optimization [J].

Liang, Shide ;

Zhang, Chi ;

Standley, Daron M. .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 (07) :2260-2267

[7] Protein Side Chain Modeling with Orientation-Dependent Atomic Force Fields Derived by Series Expansions [J].

Liang, Shide ;

Zhou, Yaoqi ;

Grishin, Nick ;

Standley, Daron M. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, 32 (08) :1680-1686

[8] OPUS-Rota: A fast and accurate method for side-chain modeling [J].

Lu, Mingyang ;

Dousis, Athanasios D. ;

Ma, Jianpeng .

PROTEIN SCIENCE, 2008, 17 (09) :1576-1585

[9] Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library [J].

Peterson, RW ;

Dutton, PL ;

Wand, AJ .

PROTEIN SCIENCE, 2004, 13 (03) :735-751

[10] Minimizing and learning energy functions for side-chain prediction [J].

Yanover, Chen ;

Schueler-Furman, Ora ;

Weiss, Yair .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2008, 15 (07) :899-911

← 1 →