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WHISCY: What information does surface conservation yield? Application to data‐driven docking
Author(s) -
de Vries Sjoerd J.,
van Dijk Aalt D.J.,
Bonvin Alexandre M.J.J.
Publication year - 2006
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.20842
Subject(s) - docking (animal) , macromolecular docking , chemistry , biological system , protein–ligand docking , computer science , computational chemistry , molecular dynamics , virtual screening , biology , medicine , nursing
Protein–protein interactions play a key role in biological processes. Identifying the interacting residues is a first step toward understanding these interactions at a structural level. In this study, the interface prediction program WHISCY is presented. It combines surface conservation and structural information to predict protein–protein interfaces. The accuracy of the predictions is more than three times higher than a random prediction. These predictions have been combined with another interface prediction program, ProMate [Neuvirth et al. J Mol Biol 2004;338:181–199], resulting in an even more accurate predictor. The usefulness of the predictions was tested using the data‐driven docking program HADDOCK [Dominguez et al. J Am Chem Soc 2003;125:1731–1737] in an unbound docking experiment, with the goal of generating as many near‐native structures as possible. Unrefined rigid body docking solutions within 10 Å ligand RMSD from the true structure were generated for 22 out of 25 docked complexes. For 18 complexes, more than 100 of the 8000 generated models were correct. Our results demonstrates the potential of using interface predictions to drive protein–protein docking. Proteins 2006. © 2006 Wiley‐Liss, Inc.