We present an alchemical enhanced sampling (ACES) method implemented in the GPU-
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …

The development of accurate transferable force fields is key to realizing the full potential of
atomistic modeling in the study of biological processes such as protein–ligand binding for …

Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …

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

Alchemical absolute binding free energy calculations are of increasing interest in drug
discovery. These calculations require restraints between the receptor and ligand to restrict …

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

Ligand binding free energy simulations (LB-FES) have been routine tasks in modern drug
discovery campaign. A long-standing challenge for LB-FES is the difficulty in adequately …

Uncertainty quantification (UQ) is rapidly becoming a sine qua non for all forms of
computational science out of which actionable outcomes are anticipated. Much of the …

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 …

We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation
of alchemical free-energy differences. We propose a software implementation and …