ArticleJournal of computational chemistry2013
Parameterization of a geometric flow implicit solvation model.
Article in Journal of computational chemistry, 2013. 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.
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- 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
- Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.Journal of chemical theory and computation · 2024Article
- A review of mathematical representations of biomolecular data.Physical chemistry chemical physics : PCCP · 2020Review
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- An efficient second-order poisson-boltzmann method.Journal of computational chemistry · 2019Article
- DG-GL: Differential geometry-based geometric learning of molecular datasets.International journal for numerical methods in biomedical engineering · 2019Article
- Improvements to the APBS biomolecular solvation software suite.Protein science : a publication of the Protein Society · 2018Article
- Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.The journal of physical chemistry. B · 2017Article
- Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.Biophysical journal · 2015Article
- Parameter optimization in differential geometry based solvation models.The Journal of chemical physics · 2015Article
- Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.The journal of physical chemistry. B · 2014Article
- Multiscale Multiphysics and Multidomain Models I: Basic Theory.Journal of theoretical & computational chemistry · 2013Article
- Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies.The Journal of chemical physics · 2013Article
- Multiscale multiphysics and multidomain models--flexibility and rigidity.The Journal of chemical physics · 2013Article
- Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.Computational & theoretical chemistry · 2013Article
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5 authors.
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Abstract
Implicit solvent models are popular for their high computational efficiency and simplicity over explicit solvent models and are extensively used for computing molecular solvation properties. The accuracy of implicit solvent models depends on the geometric description of the solute-solvent interface and the solvent dielectric profile that is defined near the surface of the solute molecule. Typically, it is assumed that the dielectric profile is spatially homogeneous in the bulk solvent medium and varies sharply across the solute-solvent interface. However, the specific form of this profile is often described by ad hoc geometric models rather than physical solute-solvent interactions. Hence, it is of significant interest to improve the accuracy of these implicit solvent models by more realistically defining the solute-solvent boundary within a continuum setting. Recently, a differential geometry-based geometric flow solvation model was developed, in which the polar and nonpolar free energies are coupled through a characteristic function that describes a smooth dielectric interface profile across the solvent-solute boundary in a thermodynamically self-consistent fashion. The main parameters of the model are the solute/solvent dielectric coefficients, solvent pressure on the solute, microscopic surface tension, solvent density, and molecular force-field parameters. In this work, we investigate how changes in the pressure, surface tension, solute dielectric coefficient, and choice of different force-field charge and radii parameters affect the prediction accuracy for hydration free energies of 17 small organic molecules based on the geometric flow solvation model. The results of our study provide insights on the parameterization, accuracy, and predictive power of this new implicit solvent model.
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