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Abstract The Poisson–Boltzmann (PB) model is a widely used electrostatic model for biomolecular solvation analysis. Formulated as an elliptic interface problem, the PB model can be numerically solved on either Eulerian meshes using finite difference/finite element methods or Lagrangian meshes using boundary element methods. Molecular surface generators, which produce the discretized dielectric interfaces between solutes and solvents, are critical factors in determining the accuracy and efficiency of the PB solvers. In this work, we investigate the utility of the Eulerian Solvent Excluded Surface (ESES) software for rendering conjugated Eulerian and Lagrangian surface representations, which enables us to numerically validate and compare the quality of Eulerian PB solvers, such as the MIBPB solver, and the Lagrangian PB solvers, such as the TABI‐PB solver. Furthermore, with the ESES software and its associated PB solvers, we are able to numerically validate an interesting and useful but often neglected source‐target symmetric property associated with the linearized PB model.
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Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver
Abstract The Poisson–Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of solvated biomolecules. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent‐excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the model. This work compares the performance of the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules. While MSMS produces triangles of exceedingly small area and large aspect ratio, the two codes yield comparable values for the SES surface area and electrostatic solvation energy, where the latter calculations were performed using the treecode‐accelerated boundary integral (TABI) PB solver. However we found that NanoShaper is computationally more efficient and reliable than MSMS, especially when parameters are set to produce highly resolved triangulations.
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- Award ID(s):
- 1819094
- PAR ID:
- 10451094
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Journal of Computational Chemistry
- Volume:
- 42
- Issue:
- 22
- ISSN:
- 0192-8651
- Page Range / eLocation ID:
- p. 1552-1560
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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