Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.

Abstract excerpt

We present the Alchemical Transfer with Coordinate Swapping (ATS) method to enable the calculation of the relative binding free energies between large congeneric ligands and single-point mutant peptides to protein receptors with the Alchemical Transfer Method (ATM) framework. Similarly to ATM, the new method implements the alchemical transformation as a coordinate transformation and works with any unmodified...

Topics

• Ligands
• Thermodynamics
• Protein Binding
• Molecular Dynamics Simulation
• Mutation
• Proteins