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	Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin
	Xie, Bin-Bin1,2; Chen, Xiu-Lan1,2; Zhang, Xi-Ying1,2; He, Hai-Lun1,2; Zhang, Yu-Zhong1,2; Zhou, Bai-Cheng2,3
刊名	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
	2008-05-15
卷号	71期号:3页码:1461-1474
关键词	Protein Interaction Interfaces Correlation Subtilisin Phycocyanin
ISSN号	0887-3585
DOI	10.1002/prot.21836
文献子类	Article
英文摘要	Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.; Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.
URL标识	查看原文
语种	英语
WOS记录号	WOS:000255269200035
公开日期	2010-12-30
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/6301]
专题	海洋研究所_实验海洋生物学重点实验室
作者单位	1.Shandong Univ, State Key Lab Microbial Technol, Jinan 250100, Peoples R China 2.Shandong Univ, Marine Biotechnol Res Ctr, Jinan 250100, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Xie, Bin-Bin,Chen, Xiu-Lan,Zhang, Xi-Ying,et al. Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2008,71(3):1461-1474.
APA	Xie, Bin-Bin,Chen, Xiu-Lan,Zhang, Xi-Ying,He, Hai-Lun,Zhang, Yu-Zhong,&Zhou, Bai-Cheng.(2008).Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,71(3),1461-1474.
MLA	Xie, Bin-Bin,et al."Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 71.3(2008):1461-1474.

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