Entropy-enthalpy compensation: Role and ramifications for rational ligand design

John D. Chodera and David L. Mobley.
Annu. Rev. Biophys. 42:121, 2013. [DOI] [PDF]

Entropy-enthalpy compensation is likely a universal phenomena, but not as severe as widely thought, and likely not of enormous concern for drug discovery and ligand design.

Free energy methods in drug discovery and design: Progress and challenges

John D. Chodera, David L. Mobley, Michael R. Shirts, Richard W. Dixon, Kim M. Branson, and Vijay S. Pande.
Curr. Opin. Struct. Biol. 21:150, 2011. [DOI] [PDF]

A review of the opportunities and challenges for alchemical free energy calculations in drug discovery and design.

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

Michael R. Shirts, David L. Mobley, John D. Chodera, and Vijay S. Pande.  
J. Phys. Chem. B 111:13052, 2007. [DOI] [PDF]

We identify a major source of systematic error in absolute alchemical free energy calculations of ligand binding and show how a simple procedure can inexpensively and accurately eliminate it.