Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Kai Wang K, John D. Chodera, Yanzhi Yang, and Michael R. Shirts. 
J. Comput. Aid. Mol. Des. 27:989, 2013. [DOI] [PDF]

We show how bound ligand poses can be identified even when the location of the binding sites are unknown using the machinery of alchemical modern free energy calculations on graphics processors. 

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.