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GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1
Author(s) -
Gardiner Eleanor J.,
Willett Peter,
Artymiuk Peter J.
Publication year - 2003
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.10386
Subject(s) - surface protein , complementarity (molecular biology) , docking (animal) , computational biology , genetic algorithm , algorithm , computer science , biology , chemistry , genetics , machine learning , virology , medicine , nursing
As part of the first Critical Assessment of PRotein Interactions, round 1, we predict the structure of two protein–protein complexes, by using a genetic algorithm, GAPDOCK, in combination with surface complementarity, buried surface area, biochemical information, and human intervention. Among the five models submitted for target 1, HPr phosphocarrier protein ( B. subtilis ) and the hexameric HPr kinase ( L. lactis ), the best correctly predicts 17 of 52 interprotein contacts, whereas for target 2, bovine rotavirus VP6 protein‐monoclonal antibody, the best model predicts 27 of 52 correct contacts. Given the difficult nature of the targets, these predictions are very encouraging and compare well with those obtained by other methods. Nevertheless, it is clear that there is a need for improved methods for distinguishing between “correct” and “plausible but incorrect” complexes. Proteins 2003;52:10–14. © 2003 Wiley‐Liss, Inc.