title: Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
abstract: Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
authors: Chemical Physics and Mateiral Physics Graduate Program, University of California, Irvine, CA, 92697 ; Department of Chemistry, University of California, Irvine, CA, 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697.
authors: Wesley M
authors: WM
authors: Botello-Smith
authors: Xingping
authors: X
authors: Liu
authors: Qin
authors: Q
authors: Cai
authors: Zhilin
authors: Z
authors: Li
authors: Hongkai
authors: H
authors: Zhao
authors: Ray
authors: R
authors: Luo
keywords: Poisson-Boltzmann; continuum membrane model; implicit solvation; membrane proteins