title: A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.
abstract: The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.
authors.affiliation: Mechanical Engineering, Boston University, Boston, MA, 02215 U.S.A.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Cooper
authors.affiliation: Electrical and Computer Engineering, Northeastern University, Boston, MA, 02115 U.S.A.
authors.forename: Jaydeep P
authors.initials: JP
authors.lastname: Bardhan
authors.affiliation: Mechanical Engineering, Boston University, Boston, MA, 02215 U.S.A.
authors.forename: L A
authors.initials: LA
authors.lastname: Barba
keywords: CUDA; Poisson-Boltzmann; Python; biomolecular electrostatics; boundary element method; implicit solvent; treecode