Drug discovery aims to select proper targets and drug candidates to address unmet clinical
needs. The end-to-end drug discovery process includes all stages of drug discovery from …

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 …

We determined the effectiveness of absolute binding free energy (ABFE) calculations to
refine the selection of active compounds in virtual compound screening, a setting where the …

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 …

Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …

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 …

Molecular dynamics (MD) simulations of proteins are commonly used to sample from the
Boltzmann distribution of conformational states, with wide-ranging applications spanning …