While conformational landscapes of biological macromolecules are often represented along physical variables, some key processes, such as solvation and molecular recognition, are best represented in terms of non-physical thermodynamic pathways. In alchemical transformations, the system is forced to explore regions of the parameter space lacking physical counterparts and which require specialized statistical mechanics formulations and simulation algorithms. We will review the history of the field ending with our recent efforts in this area, with a focus on the developments originating from Ronald Levy's laboratory. The presentation will cover early work on electrostatics and hydration theories and will then move on to alchemical methods for protein-ligand binding free energy estimation, parallel conformational sampling algorithms, and recent developments in alchemical statistical mechanics theory.

Exploring alchemical landscapes

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ACS Spring 2023

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