A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
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ABSTRACT:
SUBMITTER: Yamagishi J
PROVIDER: S-EPMC4263261 | biostudies-literature | 2014 Nov
REPOSITORIES: biostudies-literature
Publications
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
Yamagishi Junya J Okimoto Noriaki N Morimoto Gentaro G Taiji Makoto M
Journal of computational chemistry 20140915 29
The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were opti ...[more]
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