Cluster Optimization in Protein Docking

Thursday, July 26, 2007 - 3:50pm - 4:10pm
EE/CS 3-180
Julie Mitchell (University of Wisconsin, Madison)
Recent progress in obtaining docked protein complexes will be discussed.
The combination of exhaustive search, clustering and localized global
optimization can reliably find energy minima to highly nonconvex biomolecular
energy functions. Using an energy function that adds desolvation and
screened electrostatics to classical molecular mechanics potentials, the
global minimum is found very near to the observed native state. This is
demonstrated across a large number of benchmark examples.