Are current docking methods capable of building complexes from putative component
protein structures? Results of recent computational studies, including those of the CAPRI …

Empirical residue–residue pair potentials are used to screen possible complexes for protein–
protein dockings. A correct docking is defined as a complex with not more than 2.5 Å …

We present a new version of the Protein–Protein Docking Benchmark, reconstructed from
the bottom up to include more complexes, particularly focusing on more unbound–unbound …

Based on the results of several groups using different docking methods, the key properties
that determine the expected success rate in protein–protein docking calculations are …

A modeling analysis has been conducted to assess the determinants of binding strength and
specificity for three crystal complexes; the anti-hen egg white lysozyme antibody D1. 3 …

This article summarizes computer-aided analyses of X-ray crystallographic data aimed at
understanding the immunologically important aspects of the structure of antibody combining …

The methods of continuum electrostatics are used to calculate the binding free energies of a
set of protein–protein complexes including experimentally determined structures as well as …

Several potential applications of structural biology depend on discovering how one
macromolecule might recognize a partner. Experiment remains the best way to answer this …

Abstract Decoys As the Reference State (DARS) is a simple and natural approach to the
construction of structure-based intermolecular potentials. The idea is generating a large set …

Antibodies are a class of proteins indispensable for the vertebrate immune system. The
general architecture of all antibodies is very similar, but they contain a hypervariable region …