Comparison of the <scp>MSMS</scp> and <scp>NanoShaper</scp> molecular surface triangulation codes in the <scp>TABI</scp> Poisson–Boltzmann solver

Wilson, Leighton; Krasny, Robert

doi:10.1002/jcc.26692

Cited by 5 publications

(1 citation statement)

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“…Such representations are especially suitable for boundary integral methods, and a comparison between the popular MSMS and NanoShaper has been conducted in Reference 41. When the Eulerian representation is needed, additional work is required to find intersection of the mesh line and its normal direction by very challenging interpolation schemes 42,43 …”

Section: Introductionmentioning

confidence: 99%

Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES

Ullah,

Yang,

Jones

et al. 2023

J Comput Chem

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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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Section: Introductionmentioning

confidence: 99%

Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES

Ullah,

Yang,

Jones

et al. 2023

J Comput Chem

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sesA: A Program for the Analytic Computation of Solvent‐Excluded Surface Areas**

Wang

2024

ChemistryOpen

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The surface area of a molecule, an inherent geometric property of its structure, plays important roles in its solvation and functioning. Here we present an accurate and robust program, sesA, for the analytic computation of solvent‐excluded surface (SES) areas. The accuracy and robustness are achieved through the analytic computations of all the solvent‐accessible surface (SAS) regions for a surface atom and probe‐probe intersections. The detailed comparisons of the areas for a large set of protein structures by sesA and msms, a de‐facto standard for analytic SAS and SES computations, confirm sesA’s accuracy to a good extent and in the same time reveal significant differences between them. The unprecedented accuracy and robustness of sesA make it possible to analyze in great detail the surface areas of any molecules in general and biomolecules in particular.

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TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver

Wilson¹,

Geng

Krasny

2022

J. Phys. Chem. B

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This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy. The new implementation utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a fast multipole method based on barycentric Lagrange interpolation and dual tree traversal. Performance-critical portions of the code were implemented on a GPU. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code’s accuracy and efficiency.

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Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver

Cited by 5 publications

References 43 publications

Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES

Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES

sesA: A Program for the Analytic Computation of Solvent‐Excluded Surface Areas**

TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver

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