Fast Methods for Biomolecule Charge Optimization

J. P. Bardhan, J. H. Lee, S. S. Kuo, M. D. Altman, B. Tidor, J. K. White
EECS, MIT, US

Keywords: charge optimization, boundary element methods, primal-dual methods, matrix-free, fast methods

Abstract:
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.

NSTI Nanotech 2003 Conference Technical Program Abstract