Deep eutectic solvents (DESs) have recently gained increased attention for their potential in
biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …

The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

It is increasingly widely recognized that ensemble-based approaches are required to
achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose …

Accurate prediction of protein stability upon a point mutation has important applications in
drug discovery and personalized medicine. It remains a challenging issue in computational …

We subject a series of five protein–ligand systems which contain important SARS-CoV-2
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …

In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many
typical calculations, including the molecular surface, electrostatic potential, solvation free …

The advances in ligand binding affinity prediction have been fostered by system generation
tools and improved force fields (FFs). CHARMM-GUI Free Energy Calculator provides input …

Free energy calculations for protein–ligand complexes have become widespread in recent
years owing to several conceptual, methodological and technological advances. Central …

Optimization of binding affinities for ligands to their target protein is a primary objective in
rational drug discovery. Herein, we report on a collaborative study that evaluates various …