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, Pablo Chacon

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89 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)2544-2551
Number of pages8
JournalBioinformatics
Volume25
Issue number19
DOIs
StatePublished - 2009

Bibliographical note

Funding Information:
Funding: Spain grants BFU2007-65977 and CAM-BIO-0214-2006 (to P.C.) and BIO2008-02882 (to J.F.R.) and by NIH grant R01-GM071872 (to R.A.).

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