LS-VISM: A software package for analysis of biomolecular solvation

Journal of Computational Chemistry
Shenggao ZhouJ Andrew McCammon

Abstract

We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson-Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, workflow of the codes, and the postprocessing of output data. Our demo application to a host-guest system illustrates ho...Continue Reading

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Citations

Dec 10, 2015·Journal of Chemical Information and Modeling·Zuojun GuoLi Xing
May 6, 2015·Journal of Chemical Theory and Computation·Zuojun GuoJianwei Che
Oct 10, 2015·The Journal of Chemical Physics·Bao Wang, G W Wei
Aug 9, 2016·The Journal of Chemical Physics·Shenggao ZhouJ Andrew McCammon
Jun 15, 2017·The Journal of Physical Chemistry. B·Clarisse G RicciJ Andrew McCammon
Nov 22, 2019·Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia·Martin KolekRadim Brat
Feb 28, 2018·Frontiers in Molecular Biosciences·Clarisse Gravina RicciJ Andrew McCammon
Nov 13, 2015·Journal of Computational Chemistry·Alexander CumberworthJörg Gsponer
Aug 26, 2018·Journal of Computational Chemistry·Jalal Z A LalooPonnadurai Ramasami
Nov 19, 2020·Physical Chemistry Chemical Physics : PCCP·Piotr BatysZbigniew Adamczyk
Feb 19, 2021·Computational and Structural Biotechnology Journal·Shengjie SunLin Li

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