Refining near-native protein-protein docking decoys by local resampling and energy minimization

doi:10.1002/prot.22343

IOCAS-IR > 实验海洋生物学重点实验室

	Refining near-native protein-protein docking decoys by local resampling and energy minimization
	Liang, Shide 1,2,3; Wang, Guangce 3; Zhou, Yaoqi 1,2
	2009-08-01
发表期刊	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
ISSN	0887-3585
卷号	76 期号:2 页码:309-316
文章类型	Article
摘要	How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.; How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.
关键词	Docking Structure Refinement Local Resampling Energy Score
学科领域	Biochemistry & Molecular Biology ; Biophysics
DOI	10.1002/prot.22343
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000266966300004
引用统计	被引频次：9[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/2942
专题	实验海洋生物学重点实验室
作者单位	1.Indiana Univ Purdue Univ, Indiana Univ, Sch Informat, Indianapolis, IN 46202 USA 2.Indiana Univ, Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA 3.Chinese Acad Sci, Key Lab Expt Marine Biol, Inst Oceanol, Qingdao 266071, Peoples R China
第一作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Liang, Shide,Wang, Guangce,Zhou, Yaoqi. Refining near-native protein-protein docking decoys by local resampling and energy minimization[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2009,76(2):309-316.
APA	Liang, Shide,Wang, Guangce,&Zhou, Yaoqi.(2009).Refining near-native protein-protein docking decoys by local resampling and energy minimization.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,76(2),309-316.
MLA	Liang, Shide,et al."Refining near-native protein-protein docking decoys by local resampling and energy minimization".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 76.2(2009):309-316.

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