Extending the scope of alchemical perturbation methods for ligand binding free energy calculations
Previously, a method for computing binding free energies between different poses of a ligand bound to a protein using alchemical perturbation was developed. The methodology is to perturb the ligand into a smaller version, common to both poses, from which the difference in free energy between poses can be computed. Here, the method is further improved by finding low-error setups for the method, by