FRODOCK: a new approach for fast rotational protein-protein docking.
BACKGROUND
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.


BACKGROUND
http://sbg.cib.csic.es/Software/FRODOCK/
Garzon
José Ignacio
JI
Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9. 28040 Madrid, Spain.
Lopéz-Blanco
José Ramón
JR
Pons
Carles
C
Kovacs
Julio
J
Abagyan
Ruben
R
Fernandez-Recio
Juan
J
Chacon
Pablo
P
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins