The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen...

The CAPRI Challenge is a blind test of protein-protein-docking algorithms that predict the complex structure from the crystal structures of the interacting proteins. We participated in both rounds of this blind test and submitted predictions for all seven targets, relying mainly on our Fast Fourier Transform based algorithm ZDOCK that combines shape complementarity, desolvation, and electrostatics. Our group made good predictions for three...

We have developed a nonredundant benchmark for testing protein-protein docking algorithms. Currently it contains 59 test cases: 22 enzyme-inhibitor complexes, 19 antibody-antigen complexes, 11 other complexes, and 7 difficult test cases. Thirty-one of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme-inhibitor, 5 antibody-antigen, 5 others, and 5 difficult. Such...

Shape complementarity is the most basic ingredient of the scoring functions for protein-protein docking. Most grid-based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and...

A comprehensive docking study was performed on 27 distinct protein-protein complexes. For 13 test systems, docking was performed with the unbound X-ray structures of both the receptor and the ligand. For the remaining systems, the unbound X-ray structure of only molecule was available; therefore the bound structure for the other molecule was used. Our method optimizes desolvation, shape complementarity, and electrostatics using a Fast Fourier...