Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver
© 2021 Wiley Periodicals LLC.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 42(2021), 22 vom: 15. Aug., Seite 1552-1560 |
|---|---|
| 1. Verfasser: | |
| Weitere Verfasser: | |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2021
|
| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Poisson-Boltzmann boundary element method electrostatics solvated biomolecule solvent excluded surface treecode |
| Zusammenfassung: | © 2021 Wiley Periodicals LLC. 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 |
|---|---|
| Beschreibung: | Date Completed 10.01.2022 Date Revised 10.01.2022 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.26692 |