A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model
Copyright © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 35(2014), 29 vom: 05. Nov., Seite 2132-9 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Poisson-Boltzmann implicit solvent continuum electrostatics implicit solvent molecular modeling solvation-free energy Peptides Proteins Solvents |
| Zusammenfassung: | Copyright © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. 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 optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules |
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| Beschreibung: | Date Completed 28.05.2015 Date Revised 10.05.2024 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23728 |