Hierarchical molecular interfaces and solvation electrostatics

Electrostatic interactions play a significant role in determining the binding affinity of molecules and drugs. While significant effort has been devoted to the accurate computation of biomolecular electrostatics based on an all-atomic solution of the Poisson-Boltzmann (PB) equation for smaller proteins and nucleic acids, relatively little has been done to optimize the efficiency of electrostatic energetics and force computations of macromolecules at varying resolutions (also called coarse-graining). We have developed an efficient and comprehensive framework for computing coarse-grained PB electrostatic potentials, polarization energetics and forces for smooth multi-resolution representations of almost all molecular structures, available in the PDB. Important aspects of our framework include the use of variational methods for generating C2 -smooth and multi-resolution molecular surfaces (as dielectric interfaces), a parameterization and discretization of the PB equation using an alge...

• Type: Conference
• Year: 2009
• Where: SMA
• Authors: Chandrajit L. Bajaj, Shun-Chuan Albert Chen, Guoliang Xu, Qin Zhang, Wenqi Zhao
• Keywords: Electrostatic, Electrostatic Energetics, PB Electrostatic Potentials, SMA 2009, Solid Modeling