title: Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.
abstract: Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membranes into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multigrid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations.
authors.affiliation: Chemical Physics and Materials Physics Graduate Program, ‡Department of Chemistry, §Department of Molecular Biology and Biochemistry, ∥Department of Biomedical Engineering, and ⊥Department of Chemical Engineering and Materials Science, University of California , Irvine, California 92697, United States.
authors.forename: Wesley M
authors.initials: WM
authors.lastname: Botello-Smith
authors.affiliation: Chemical Physics and Materials Physics Graduate Program, ‡Department of Chemistry, §Department of Molecular Biology and Biochemistry, ∥Department of Biomedical Engineering, and ⊥Department of Chemical Engineering and Materials Science, University of California , Irvine, California 92697, United States.
authors.forename: Ray
authors.initials: R
authors.lastname: Luo
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular
chemical_list: D008024:Ligands; D008565:Membrane Proteins