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Highly accurate biomolecular electrostatics in continuum dielectric environments
Author(s) -
Zhou Y. C.,
Feig Michael,
Wei G. W.
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20769
Subject(s) - electrostatics , dielectric , static electricity , molecular dynamics , electrostatic interaction , chemical physics , nanotechnology , materials science , computational chemistry , chemistry , physics , quantum mechanics , optoelectronics
Implicit solvent models based on the Poisson‐Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson‐Boltzmann solver is developed based on the matched interface and boundary (MIB) method, which rigorously enforces the continuity conditions of both the electrostatic potential and its flux at the molecular surface. The MIB based PB solver attains much better convergence rates as a function of mesh size compared to conventional finite difference and finite element based PB solvers. Consequently, highly accurate electrostatic potentials and solvation energies are obtained at coarse mesh sizes. In the context of biomolecular electrostatic calculations it is demonstrated that the MIB method generates substantially more accurate solutions of the PB equation than other established methods, thus providing a new level of reference values for such models. Initial results also indicate that the MIB method can significantly improve the quality of electrostatic surface potentials of biomolecules that are frequently used in the study of biomolecular interactions based on experimental structures. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008