Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …

We discuss basic physical–chemical principles underlying the formation of stable
macromolecular complexes, which in many cases are likely to be the biological units …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Determination of side-chain conformations is an important step in protein structure prediction
and protein design. Many such methods have been presented, although only a small …

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 …

The docking field has come of age. The time is ripe to present the principles of docking,
reviewing the current state of the field. Two reasons are largely responsible for the maturity …

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 …

▪ Abstract Molecular docking is an invaluable tool in modern drug discovery. This review
focuses on methodological developments relevant to the field of molecular docking. The …

Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …