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 …

The accurate scoring of rigid‐body docking orientations represents one of the major
difficulties in protein–protein docking prediction. Other challenges are the development of …

A protein docking study was performed for two classes of biomolecular complexes: six
enzyme/inhibitor and four antibody/antigen. Biomolecular complexes for which crystal …

Here we carry out an examination of shape complementarity as a criterion in protein‐protein
docking and binding. Specifically, we examine the quality of shape complementarity as a …

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 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 …

A matching algorithm using surface complementarity between receptor and ligand protein
molecules is outlined. The molecular surfaces are represented by “critical points,” describing …

A new version of GRAMM was applied to Targets 14, 18, and 19 in CAPRI Round 5. The
predictions were generated without manual intervention. Ten top‐ranked matches for each …

Protein–protein docking algorithms provide a means to elucidate structural details for
presently unknown complexes. Here, we present and evaluate a new method to predict …

Rigid-body docking of two molecules involves matching of their surfaces. A successful
docking methodology considers two key issues: molecular surface representation, and …