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Bioinformatics Advance Access originally published online on July 20, 2009
Bioinformatics 2009 25(19):2544-2551; doi:10.1093/bioinformatics/btp447
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FRODOCK: a new approach for fast rotational protein–protein docking

José Ignacio Garzon 1, José Ramón Lopéz-Blanco 1, Carles Pons 2,3, Julio Kovacs 4,{dagger}, Ruben Abagyan 4, Juan Fernandez-Recio 2 and Pablo Chacon 1,*

1Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain, 2Barcelona Supercomputing Center, 3National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 29, Barcelona 08034, Spain and 4Department of Molecular Biology, The Scripps Research Institute La Jolla, CA 92037, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Prediction of protein–protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of the initial exhaustive search. In this approach we combine the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations to accelerate the search. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. The interaction-energy minima are identified by a novel, fast and exhaustive rotational docking search combined with a simple translational scanning. Results obtained on standard protein–protein benchmarks demonstrate its general applicability and robustness. The accuracy is comparable to that of existing state-of-the-art initial exhaustive rigid-body docking tools, but achieving superior efficiency. Moreover, a parallel version of the method performs the docking search in just a few minutes, opening new application opportunities in the current ‘omics’ world.

Availability: http://sbg.cib.csic.es/Software/FRODOCK/

Contact: Pablo{at}cib.csic.es

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

{dagger} Present address: SeaSpace Co., 12120 Kear Place, Poway, CA 92064, USA

Received on March 23, 2009; revised on July 15, 2009; accepted on July 16, 2009

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