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The accurate prediction of protein-ligand binding affinities is crucial fordrug discovery. Alchemical free energy calculations have become a popular toolfor this purpose. However, the accuracy and reliability of these methods canvary depending on the methodology. In this study, we evaluate the performanceof a relative binding free energy protocol based on the alchemical transfermethod (ATM), a novel approach based on a coordinate transformation that swapsthe positions of two ligands. The results show that ATM matches the performanceof more complex free energy perturbation (FEP) methods in terms of Pearsoncorrelation, but with marginally higher mean absolute errors. This study showsthat the ATM method is competitive compared to more traditional methods inspeed and accuracy and offers the advantage of being applicable with anypotential energy function.

Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series