Molecular Docking: Foundations in Statistical Mechanics

David Minh (mccammon.ucsd.edu/~dminh/)

I will describe implicit ligand theory, a new formalism for noncovalent binding free energies that separates the calculation into two simulation stages: (i) sampling receptor configurations and (ii) calculating the binding PMF - the affinity of a ligand to a rigid receptor - for each receptor snapshot.  Molecular docking may be interpreted as applying a dominant state approximation to each stage.  Implicit ligand theory provides a pathway for the improvement of scoring functions.  Recommended reading: http://arxiv.org/abs/1208.4885