TY - JOUR
T1 - FRODOCK
T2 - A new approach for fast rotational protein-protein docking
AU - Garzon, José Ignacio
AU - Lopéz-Blanco, José Ramón
AU - Pons, Carles
AU - Kovacs, Julio
AU - Abagyan, Ruben
AU - Fernandez-Recio, Juan
AU - Chacon, Pablo
N1 - 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.).
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=70349882144&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btp447
DO - 10.1093/bioinformatics/btp447
M3 - Article
C2 - 19620099
AN - SCOPUS:70349882144
SN - 1367-4803
VL - 25
SP - 2544
EP - 2551
JO - Bioinformatics
JF - Bioinformatics
IS - 19
ER -