title: LS-VISM: A software package for analysis of biomolecular solvation.
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 how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces.
authors.affiliation: Department of Mathematics, University of California, San Diego, La Jolla, California, 92093-0112.
authors.forename: Shenggao
authors.initials: S
authors.lastname: Zhou
authors.forename: Li-Tien
authors.initials: LT
authors.lastname: Cheng
authors.forename: Hui
authors.initials: H
authors.lastname: Sun
authors.forename: Jianwei
authors.initials: J
authors.lastname: Che
authors.forename: Joachim
authors.initials: J
authors.lastname: Dzubiella
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D001665:Binding Sites; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012995:Solubility; D012996:Solutions; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins; D012996:Solutions
keywords: Boltzmann theory; Poisson; biomolecular modeling; compact coupling interface method; dielectric boundary force; level-set method; solvation free energy; variational implicit-solvent model