Kompetenznetzwerk für wissenschaftliches Höchstleistungsrechnen in Bayern


Fast & Flexible Poisson Boltzmann Solver


Prof. Dr. G. Greiner
Computer Graphics Group (Informatik 9)
FAU Erlangen-Nürnberg


Electrostatic interactions are the dominant driving force for the stability of biomolecules, for their interactions, and thus their function. A fast and accurate assessment of the electrostatics of biomolecules is required e.g. for the calculation of binding affinities in drug discovery or protein stability analysis in enzyme design. Additionally, electrostatics is the dominant contribution in the prediction of protonation changes of amino acids in proteins e.g. in constant pH simulations. Due to insufficient configurational sampling in simulations of biomolecules including an explicit solvent environment, the protein energetics is frequently approximated using an implicit solvent. An accurate solution is provided by the numerical solution of the Poisson-Boltzmann equation. Here, we aim at the development of a fast and accurate parallelized Poisson-Boltzmann Solver making use of graphics hardware for further acceleration.