ArticleJournal of computational chemistry2014
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- The Hydrolysis Rate of Paraoxonase-1 Q and R Isoenzymes: An In Silico Study Based on In Vitro Data.Molecules (Basel, Switzerland) · 2022Article
- Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ.Molecules (Basel, Switzerland) · 2021Article
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.Journal of computational chemistry · 2018Article
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4 authors.
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Abstract
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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