Bardhan J.P., Altman M.D., Lippow S.M., Tidor B., White J.K.
Massachusetts Institute of Technology, US
Keywords: biomolecule, continuum van der Waals, curved panels, quadrature
A key step in computational drug design is the calculation of binding free energies between drug candidates and their target; one important component of these binding free energies is the van der Waals interactions that candidates and target make with solvent. Our work offers a more efficient and accurate approach to the calculation of these energies. Recently, a continuum model was introduced that expressed this van der Waals interaction energy as a sum of volume integrals; we applied the divergence theorem to reduce the problem to simpler, more efficient surface integrals. After validating the surface formulation, we improved the surface discretization by representing the molecular surface with spherical rather than flat panels, and we have developed a simple but accurate method for integrating these curved surfaces. The integration method may also be useful for boundary element simulations of biomolecules and for generalized Born calculations.
Journal: TechConnect Briefs
Volume: 1, Technical Proceedings of the 2005 NSTI Nanotechnology Conference and Trade Show, Volume 1
Published: May 8, 2005
Pages: 512 - 515
Industry sectors: Advanced Materials & Manufacturing | Medical & Biotech
Topics: Biomaterials, Informatics, Modeling & Simulation
ISBN: 0-9767985-0-6