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

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

SUBMITTER: Garzon JI 

PROVIDER: S-EPMC2800348 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature