The biological function of a protein typically depends on the structure of specific binding
sites. These sites are located at the surface of the protein molecule and are determined by …

Rapid accumulation of experimental data on protein‐protein complexes drives the paradigm
shift in protein docking from “traditional,” template free approaches to template based …

Molecular (locking is a popular way to screen for novel drug compounds. The method
involves aligning small molecules to a protein structure and estimating their binding affinity …

A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on
proteins is described. This program and the associated ones are written in Turbo Pascal and …

There is currently great interest in comparing protein–ligand docking programs. A review of
recent comparisons shows that it is difficult to draw conclusions of general applicability …

Rigid-body docking has become quite successful in predicting the correct conformations of
binary protein complexes, at least when the constituent proteins do not undergo large …

We present an updated and integrated version of our widely used protein–protein docking
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …

The computer-based design of protein–protein interactions is a rigorous test of our
understanding of molecular recognition and an attractive approach for creating novel tools …

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 …

Traditional approaches to protein–protein docking sample the binding modes with no regard
to similar experimentally determined structures (templates) of protein–protein complexes …