Consensus scoring for enriching near-native structures from protein-protein docking decoys

doi:10.1002/prot.22252

IOCAS-IR > 实验海洋生物学重点实验室

	Consensus scoring for enriching near-native structures from protein-protein docking decoys
	Liang, Shide 1,2,3,4; Meroueh, Samy O.2,3; Wang, Guangce 4; Qiu, Chao 4; Zhou, Yaoqi 1,2,3
	2009-05-01
发表期刊	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
ISSN	0887-3585
卷号	75 期号:2 页码:397-403
文章类型	Article
摘要	The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.; The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.
关键词	Protein Docking Near Native Decoy Selection Energy Score Interface Propensity Conservation Score
学科领域	Biochemistry & Molecular Biology ; Biophysics
DOI	10.1002/prot.22252
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000264169400012
引用统计	被引频次：28[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/337002/2940
专题	实验海洋生物学重点实验室
作者单位	1.Indiana Univ Purdue Univ, Sch Informat, Indianapolis, IN 46202 USA 2.Indiana Univ Sch Med, Dept Biochem & Mol Biol, Indianapolis, IN 46202 USA 3.Indiana Univ Sch Med, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA 4.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,Meroueh, Samy O.,Wang, Guangce,et al. Consensus scoring for enriching near-native structures from protein-protein docking decoys[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2009,75(2):397-403.
APA	Liang, Shide,Meroueh, Samy O.,Wang, Guangce,Qiu, Chao,&Zhou, Yaoqi.(2009).Consensus scoring for enriching near-native structures from protein-protein docking decoys.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,75(2),397-403.
MLA	Liang, Shide,et al."Consensus scoring for enriching near-native structures from protein-protein docking decoys".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 75.2(2009):397-403.

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