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	Refining near-native protein-protein docking decoys by local resampling and energy minimization
	Liang, Shide1,2,3; Wang, Guangce3; Zhou, Yaoqi1,2
刊名	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
	2009-08-01
卷号	76期号:2页码:309-316
关键词	Docking Structure Refinement Local Resampling Energy Score
ISSN号	0887-3585
DOI	10.1002/prot.22343
文献子类	Article
英文摘要	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.
学科主题	Biochemistry & Molecular Biology ; Biophysics
URL标识	查看原文
语种	英语
WOS记录号	WOS:000266966300004
公开日期	2010-12-22
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/2943]
专题	海洋研究所_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
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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