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 …

Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

Abstract Molegro Virtual Docker is a protein-ligand docking simulation program that allows
us to carry out docking simulations in a fully integrated computational package. MVD has …

This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …

Improved rational drug design methods are needed to lower the cost and increase the
success rate of drug discovery and development. Alchemical binding free energy …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …

The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the
development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA …

In this review, we outline the growing role that molecular dynamics simulation is able to play
as a design tool in drug delivery. We cover both the pharmaceutical and computational …