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 …

Continuum solvation models, such as Poisson–Boltzmann and Generalized Born methods,
have become increasingly popular tools for investigating the influence of electrostatics on …

We have developed a computer algorithm, FOLDEF (for FOLD-X energy function), to provide
a fast and quantitative estimation of the importance of the interactions contributing to the …

Structural and mutational analyses reveal a central role for electrostatic interactions in
protein–protein association. Experiment and theory both demonstrate that clusters of …

Two types of noncovalent bonding interactions are present in protein structures, specific and
nonspecific. Nonspecific interactions are mostly hydrophobic and van der Waals. Specific …

Electrostatic energies provide what is perhaps the most effective tool for structure–function
correlation of biological molecules. This review considers the current state of simulations of …

Lactate dehydrogenase (LDH) interconverts pyruvate and lactate with concomitant
interconversion of NADH and NAD+. Although crystal structures of a variety of LDH have …

Many cellular functions involve cysteine chemistry via thiol–disulfide exchange pathways.
The nucleophilic cysteines of the enzymes involved are activated as thiolate. A thiolate is …

The pKa‐cooperative aims to provide a forum for experimental and theoretical researchers
interested in protein pKa values and protein electrostatics in general. The first round of the …