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 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 …

The de novo design of small molecule–binding proteins has seen exciting recent progress;
however, high-affinity binding and tunable specificity typically require laborious screening …

We present an extension of the alchemical transfer method (ATM) for the estimation of
relative binding free energies of molecular complexes applicable to conventional, as well as …

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 …

Free energy perturbation (FEP) calculations are now routinely used in drug discovery to
estimate the relative FEB (RFEB) of small molecules to a biomolecular target of interest …

The alchemical transfer method (ATM) for the calculation of standard binding free energies
of noncovalent molecular complexes is presented. The method is based on a coordinate …

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 apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …

In this work, we review recent studies in the field of computational solvation. Methods at
different scales from ab initio to force field calculations with both implicit solvent and explicit …