期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 36, 期 14, 页码 1047-1059出版社
WILEY
DOI: 10.1002/jcc.23890
关键词
biomolecular modeling; variational implicit-solvent model; solvation free energy; Poisson; Boltzmann theory; dielectric boundary force; level-set method; compact coupling interface method
资金
- NSF [DMS-1319731]
- NIH [R01GM096188]
- NSF
- NIH
- HHMI
- NBCR (McCammon group)
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [1319731] Funding Source: National Science Foundation
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. (c) 2015 Wiley Periodicals, Inc.
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