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Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin
Author(s) -
Xie BinBin,
Chen XiuLan,
Zhang XiYing,
He HaiLun,
Zhang YuZhong,
Zhou BaiCheng
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21836
Subject(s) - protein–protein interaction , biological system , matrix (chemical analysis) , computational biology , sequence (biology) , identification (biology) , subtilisin , computer science , chemistry , physics , biology , biochemistry , botany , chromatography , enzyme
Abstract 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. Proteins 2008. © 2007 Wiley‐Liss, Inc.