Nanotech 2003 Vol. 2
Nanotech 2003 Vol. 2
Technical Proceedings of the 2003 Nanotechnology Conference and Trade Show, Volume 2

Computational Methods and Numerics Chapter 12

Fast Methods for Biomolecule Charge Optimization

Authors: J.P. Bardhan, J.H. Lee, S.S. Kuo, M.D. Altman, B. Tidor and J.K. White

Affilation: Massachusetts Institute of Technology, United States

Pages: 508 - 511

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

ISBN: 0-9728422-1-7
Pages: 600

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