In computational drug design, ranking a series of compound analogs in a manner that is
consistent with experimental affinities remains a challenge. In this study, we evaluated the …

In this work, the ability of molecular dynamics simulations (MD) to prospectively predict
regions of ligand binding sites that could undergo induced fit effects was investigated …

There is growing consensus that the optimization of the kinetic parameters for drug–protein
binding leads to improved drug efficacy. Therefore, computational methods have been …

Highlights•Drug-target binding kinetics contribute to drug efficacy.•Many molecular dynamics
approaches to studying binding kinetics have been reported.•High quality datasets enable …

Free energy calculations are used to study how strongly potential drug molecules interact
with their target receptors. The accuracy of these calculations depends on the accuracy of …

Computer-aided drug design plays an important role in medicinal chemistry to obtain
insights into molecular mechanisms and to prioritize design strategies. Although significant …

Highlights•Mixed solvent dynamics can characterise what will bind to a site on a
protein.•Dynamic docking approaches can allow for protein flexibility in ligand …

Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …

In the field of medicinal chemistry there is increasing focus on identifying key proteins whose
biochemical functions can firmly be linked to serious diseases. Such proteins become …

Computational techniques applied to drug discovery have gained considerable popularity
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …