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Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins
Author(s) -
Tillier Elisabeth R. M.,
Biro Laurence,
Li Ginny,
Tillo Desiree
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - Uncategorized
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20948
Subject(s) - phylogenetic tree , interdependence , similarity (geometry) , computational biology , computer science , evolutionary algorithm , property (philosophy) , sequence (biology) , evolutionary biology , order (exchange) , biology , genetics , artificial intelligence , philosophy , epistemology , gene , political science , law , image (mathematics) , finance , economics
Approaches for the determination of interacting partners from different protein families (such as ligands and their receptors) have made use of the property that interacting proteins follow similar patterns and relative rates of evolution. Interacting protein partners can then be predicted from the similarity of their phylogenetic trees or evolutionary distances matrices. We present a novel method called Codep, for the determination of interacting protein partners by maximizing co-evolutionary signals. The order of sequences in the multiple sequence alignments from two protein families is determined in such a manner as to maximize the similarity of substitution patterns at amino acid sites in the two alignments and, thus, phylogenetic congruency. This is achieved by maximizing the total number of interdependencies of amino acids sites between the alignments. Once ordered, the corresponding sequences in the two alignments indicate the predicted interacting partners. We demonstrate the efficacy of this approach with computer simulations and in analyses of several protein families. A program implementing our method, Codep, is freely available to academic users from our website: http://www.uhnresearch.ca/labs/tillier/.