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GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1

Gardiner, E.J., Willett, P. and Artymiuk, P.J. (2003) GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1. Proteins: Structure, Function, and Genetics, 52 (1). pp. 10-14.


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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.

Item Type: Article
Copyright, Publisher and Additional Information: © 2003 Wiley-Liss, Inc. This is an author produced version of a paper published in Proteins: Structure, Function, and Genetics. Uploaded in accordance with the publisher's self-archiving policy.
Keywords: docking competition, protein-protein interaction, protein-protein docking, shape complementarity, molecular recognition
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield)
The University of Sheffield > University of Sheffield Research Centres and Institutes > The Krebs Institute for Biomolecular Research (Sheffield)
The University of Sheffield > Faculty of Science (Sheffield) > Department of Chemistry (Sheffield)
The University of Sheffield > Faculty of Science (Sheffield) > School of Biological Sciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield)
Depositing User: Sherpa Assistant
Date Deposited: 24 Jan 2008 17:10
Last Modified: 08 Feb 2013 16:55
Published Version: http://dx.doi.org/10.1002/prot.10386
Status: Published
Publisher: John Wiley & Sons, Inc.
Refereed: Yes
Identification Number: 10.1002/prot.10386
URI: http://eprints.whiterose.ac.uk/id/eprint/3590

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