Title | ||
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A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers. |
Abstract | ||
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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 apbsfinite-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 apbssolver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is on the order of 1–2% error, when running on one gpu card (nvidiaTesla C2075), compared with apbsrunning 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. |
Year | DOI | Venue |
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2014 | 10.1016/j.cpc.2013.10.028 | Computer Physics Communications |
Keywords | Field | DocType |
Biomolecular electrostatics,Implicit solvent,Poisson–Boltzmann,Boundary element method,Treecode,Python,CUDA | Poisson–Boltzmann equation,Computer science,Xeon Phi,CUDA,Computational science,Hardware acceleration,Boundary element method,Xeon,Solver,Python (programming language) | Journal |
Volume | Issue | ISSN |
185 | 3 | 0010-4655 |
Citations | PageRank | References |
5 | 0.64 | 10 |
Authors | ||
3 |
Name | Order | Citations | PageRank |
---|---|---|---|
Christopher D. Cooper | 1 | 6 | 1.01 |
Jaydeep P. Bardhan | 2 | 56 | 8.55 |
Lorena A. Barba | 3 | 52 | 7.70 |