Computational approaches that'dock'small molecules into the structures of macromolecular
targets and'score'their potential complementarity to binding sites are widely used in hit …

The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …

The affinities of hosts—ranging from small synthetic cavitands to large proteins—for organic
molecules are well documented. The average association constants for the binding of …

Recently, the combination of state-of-the-art molecular mechanical force fields with
continuum solvation models enables us to make relatively accurate predictions of both …

We have developed an implicit solvent effective potential (AGBNP) that is suitable for
molecular dynamics simulations and high-resolution modeling. It is based on a novel …

Implicit solvent hydration free energy models are an important component of most modern
computational methods aimed at protein structure prediction, binding affinity prediction, and …

Ligand binding affinity prediction is one of the most important applications of computational
chemistry. However, accurately ranking compounds with respect to their estimated binding …

The critical issues in docking include the prediction of the correct binding pose and the
accurate estimation of the corresponding binding affinity. Different docking methodologies …

The binding free energies (Δ G Bind) obtained from molecular mechanics with Poisson–
Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface …

The development of a new tailor-made scoring function to predict binding affinities of
protein− ligand complexes is described. Knowledge-based pair-potentials are specifically …