The Alchemical Transfer Method (ATM) is herein validated against the relative binding-free
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …

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 …

The race to meet the challenges of the global pandemic has served as a reminder that the
existing drug discovery process is expensive, inefficient and slow. There is a major …

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

We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …

The accurate prediction of protein–ligand binding affinities is crucial for drug discovery.
Alchemical free energy calculations have become a popular tool for this purpose. However …

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 present receptor hopping and receptor swapping free energy estimation protocols based
on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands …

The advent of personalised medicine promises a deeper understanding of mechanisms and
therefore therapies. However, the connection between genomic sequences and clinical …