Bardhan J.P., Lee J-H., Kuo S.S., Altman M.D., Tidor B., White J.K.
Massachusetts Institute of Technology, US
Keywords: boundary element methods, charge optimization, fast methods, matrix-free, primal-dual methods
We report a Hessian-implicit optimization method for linearly constrained quadratic programs. Our research focuses on the energetics of protein-protein interactions, and this method was developed to quickly solve the charge optimization problem: given a ligand and its complex with a receptor, determine the ligand charge distribution that minimizes the electrostatic free energy of binding. The new optimization method couples boundary element methods and primal-dual methods, initial results suggest that the method scales much better than previous methods. To the authors knowledge, this is the first demonstration of an optimization technique that uses a matrix-implicit gradient calculation.
Journal: TechConnect Briefs
Volume: 2, Technical Proceedings of the 2003 Nanotechnology Conference and Trade Show, Volume 2
Published: February 23, 2003
Pages: 508 - 511
Industry sectors: Advanced Materials & Manufacturing | Sensors, MEMS, Electronics
Topic: Informatics, Modeling & Simulation
ISBN: 0-9728422-1-7