title: GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules.
abstract: Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and, in particular, also their interactions with each other. Additionally, knowledge about solution electrostatics may also guide the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson-Boltzmann equation (PBE). Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss-Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and, thus, needs to be carefully considered, e.g., in design studies on membrane proteins.
authors.affiliation: Computer Graphics Group, Department of Computer Science, University Erlangen-Nürnberg , Erlangen , Germany ; Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Bertelshofer
authors.affiliation: Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany.
authors.forename: Liping
authors.initials: L
authors.lastname: Sun
authors.affiliation: Computer Graphics Group, Department of Computer Science, University Erlangen-Nürnberg , Erlangen , Germany.
authors.forename: Günther
authors.initials: G
authors.lastname: Greiner
authors.affiliation: Computational Biology, Department of Biology, University Erlangen-Nürnberg , Erlangen , Germany.
authors.forename: Rainer A
authors.initials: RA
authors.lastname: Böckmann
keywords: Poisson–Boltzmann equation; electrostatics; finite-difference method; membranes; molecular surface