ArticleJournal of chemical theory and computation2008
On the Dielectric Boundary in Poisson-Boltzmann Calculations.
Article in Journal of chemical theory and computation, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.ACS omega · 2022Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Explicit ions/implicit water generalized Born model for nucleic acids.The Journal of chemical physics · 2018Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.Journal of molecular graphics & modelling · 2017Article
- Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.Journal of theoretical & computational chemistry · 2014Article
- Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies.The Journal of chemical physics · 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
- Parameterization of a geometric flow implicit solvation model.Journal of computational chemistry · 2013Article
- Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?Communications in computational physics · 2013Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.Journal of computer-aided molecular design · 2011Article
- Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration.Journal of chemical theory and computation · 2010Article
- Prediction of protein solubility from calculation of transfer free energy.Biophysical journal · 2008Article
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Authors and funding
2 authors.
Funding
Abstract
In applying the Poisson-Boltzmann (PB) equation for calculating the electrostatic free energies of solute molecules, an open question is how to specify the boundary between the low-dielectric solute and the high-dielectric solvent. Two common specifications of the dielectric boundary, as the molecular surface (MS) or the van der Waals (vdW) surface of the solute, give very different results for the electrostatic free energy of the solute. With the same atomic radii, the solute is more solvent-exposed in the vdW specification. One way to resolve the difference is to use different sets of atomic radii for the two surfaces. The radii for the vdW surface would be larger in order to compensate for the higher solvent exposure. Here we show that radius re-parameterization required for bringing MS-based and vdW-based PB results to agreement is solute-size dependent. The difference in atomic radii for individual amino acids as solutes is only 2-5% but increases to over 20% for proteins with ~200 residues. Therefore two sets of radii that yield identical MS-based and vdW-based PB results for small solutes will give very different PB results for large solutes. This finding raises issues about two common practices. The first is the use of atomic radii, which are parameterized against either experimental solvation data or data obtained from explicit-solvent simulations on small compounds, for PB calculations on proteins. The second is the parameterization of vdW-based generalized Born models against MS-based PB results.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.