Informal Seminar: Friday, September 21, 10:30am, Genentech S204 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 -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak@gmail.com davidsivak.com 510-541-9006