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 …

Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

Drug discovery utilizes chemical biology and computational drug design approaches for the
efficient identification and optimization of lead compounds. Chemical biology is mostly …

The role of crystal packing in determining the observed conformations of amino acid side-
chains in protein crystals is investigated by (1) analysis of a database of proteins that have …

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 …

Rotamer libraries are widely used in protein structure prediction, protein design, and
structure refinement. As the size of the structure data base has increased rapidly in recent …

Proteins are in constant motion between different conformational states with similar
energies. This has often been ignored in drug design. However, protein flexibility is …

We review insights from computational studies of affinities of ligands binding to proteins. The
power of structural biology is in translating knowledge of protein structures into insights …

Protein interface hot spots, as revealed by alanine scanning mutagenesis, continue to
stimulate interest in the biophysical basis of molecular recognition. Although these regions …

Identifying a protein's functional sites is an important step towards characterizing its
molecular function. Numerous structure-and sequence-based methods have been …