Journal Article

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

José Ignacio Garzon, José Ramón Lopéz-Blanco, Carles Pons, Julio Kovacs, Ruben Abagyan, Juan Fernandez-Recio and Pablo Chacon

in Bioinformatics

Volume 25, issue 19, pages 2544-2551
Published in print October 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp447
FRODOCK: a new approach for fast rotational protein–protein docking

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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@cib.csic.es

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6356 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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