MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.

ABSTRACT: A hierarchical approach has been developed for protein-protein docking. In the first step, a Fast Fourier Transform (FFT)-based docking algorithm is used to globally sample all putative binding modes, in which the protein is represented by a reduced model, that is, each side chain on the protein surface is represented by its center of mass. Compared to conventional FFT docking with all-atom models, the FFT docking method with a reduced model is expected to generate more hits because it allows larger side-chain flexibility. Next, the filtered binding modes (normally several thousands) are refined by an iteratively derived knowledge-based scoring function ITScorePP and by considering backbone/loop flexibility using an ensemble docking algorithm. The distance-dependent potentials of ITScorePP

SUBMITTER: Huang SY 

PROVIDER: S-EPMC2952710 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature