ArticleCommunications in computational physics2013
Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Article in Communications in computational physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- In silico drug discovery and molecular dynamics simulation for targeting neonatal pneumonia and bronchopulmonary dysplasia.Frontiers in chemistry · 2026Article
- Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.Biophysical journal · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.Journal of computational chemistry · 2019Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.Journal of chemical information and modeling · 2017Article
- Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.Journal of computational chemistry · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.Journal of computational chemistry · 2016Article
- A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.The Journal of chemical physics · 2015Article
- Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope.The Journal of cell biology · 2015Article
- Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation.Journal of molecular modeling · 2015Article
- On the energy components governing molecular recognition in the framework of continuum approaches.Frontiers in molecular biosciences · 2015Review
- Mathematical and computational modeling in biology at multiple scales.Theoretical biology & medical modelling · 2014Review
- Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.The journal of physical chemistry. B · 2014Article
- Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.Journal of theoretical & computational chemistry · 2014Article
- On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.Journal of theoretical & computational chemistry · 2014Article
- Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond.Proteins · 2013Article
- Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.The Journal of chemical physics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.
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