Method for Computing Protein Binding Affinity
  A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding. 
Charles F. F. Karney (1), Jason E. Ferrara (1), Stephan Brunner (2)   ((1) Sarnoff Corporation, (2) Locus Pharmaceuticals)