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

TL;DR

This study compares MSMS and NanoShaper surface triangulation codes within the TABI Poisson-Boltzmann solver, finding NanoShaper more efficient and reliable despite similar surface area and energy calculations.

Contribution

It provides a systematic comparison of MSMS and NanoShaper codes for biomolecular surface triangulation in PB simulations, highlighting NanoShaper's advantages.

Findings

NanoShaper is more efficient than MSMS.

Both codes produce comparable surface area and energy results.

NanoShaper is more reliable with high-resolution triangulations.

Abstract

The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. 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 PB model. In this work we compare 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 more efficient and reliable than MSMS, especially when parameters are set to produce highly resolved triangulations.