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

Proteins
Sheng-You Huang, Xiaoqin Zou

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 were extracted by a physics-based iterative method, which circumvents the long-standing reference state problem in the knowledge-based approaches. With this hierarchical protocol, we have participated in the CAPRI experiments for Rounds 15-19 of 11 targets (T32-T42). In the predictor experiments, we achieved correct binding modes for six targets: three are with high accuracy (T40 for both distinct binding modes, T41, and T42), two are with me...Continue Reading

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