Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 60, Issue 2, Pages 275-280Publisher
WILEY
DOI: 10.1002/prot.20570
Keywords
CAPRI; blind test; protein docking; multiple sequence alignments; correlated mutations; tree determinants; conserved regions; interacting surface patches
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We have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases. (c) 2005 Wiley-Liss, Inc.
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