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Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility
Author(s) -
May Andreas,
Zacharias Martin
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.21735
Subject(s) - docking (animal) , macromolecular docking , protein–ligand docking , searching the conformational space for docking , computer science , computational biology , protein structure , biological system , chemistry , molecular dynamics , computational chemistry , biology , biochemistry , virtual screening , medicine , nursing
A reduced protein model combined with a systematic docking approach has been employed to predict protein–protein complex structures in CAPRI rounds 6–11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to the second protein starting from many thousand initial protein partner placements. It also allows for approximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precalculated soft collective backbone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two targets, and predicted >20% correct contacts for five targets. Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed. Proteins 2007. © 2007 Wiley‐Liss, Inc.