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Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver
Author(s) -
Wilson Leighton,
Krasny Robert
Publication year - 2021
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26692
Subject(s) - solver , boundary (topology) , poisson–boltzmann equation , surface (topology) , solvation , accessible surface area , boltzmann constant , set (abstract data type) , electrostatics , chemistry , computer science , computational science , physics , materials science , solvent , computational chemistry , mathematics , geometry , mathematical optimization , thermodynamics , mathematical analysis , quantum mechanics , ion , programming language , organic chemistry
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.