ArticleJournal of chemical theory and computation2014
Introducing Charge Hydration Asymmetry into the Generalized Born Model.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Deep molecular modeling and mechanistic insights into type 2A von Willebrand disease with von Willebrand factor A2 domain mutations.Research and practice in thrombosis and haemostasis · 2025Article
- Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution.The journal of physical chemistry. B · 2025Article
- 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 Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.ACS omega · 2022Article
- 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
- Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields.Journal of chemical theory and computation · 2020Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.Journal of computational chemistry · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.Journal of chemical theory and computation · 2018Article
- Building Water Models: A Different Approach.The journal of physical chemistry letters · 2014Article
- Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.The Journal of chemical physics · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The effect of charge hydration asymmetry (CHA)-non-invariance of solvation free energy upon solute charge inversion-is missing from the standard linear response continuum electrostatics. The proposed charge hydration asymmetric-generalized Born (CHA-GB) approximation introduces this effect into the popular generalized Born (GB) model. The CHA is added to the GB equation via an analytical correction that quantifies the specific propensity of CHA of a given water model; the latter is determined by the charge distribution within the water model. Significant variations in CHA seen in explicit water (TIP3P, TIP4P-Ew, and TIP5P-E) free energy calculations on charge-inverted "molecular bracelets" are closely reproduced by CHA-GB, with the accuracy similar to models such as SEA and 3D-RISM that go beyond the linear response. Compared against reference explicit (TIP3P) electrostatic solvation free energies, CHA-GB shows about a 40% improvement in accuracy over the canonical GB, tested on a diverse set of 248 rigid small neutral molecules (root mean square error, rmse = 0.88 kcal/mol for CHA-GB vs 1.24 kcal/mol for GB) and 48 conformations of amino acid analogs (rmse = 0.81 kcal/mol vs 1.26 kcal/mol). CHA-GB employs a novel definition of the dielectric boundary that does not subsume the CHA effects into the intrinsic atomic radii. The strategy leads to finding a new set of intrinsic atomic radii optimized for CHA-GB; these radii show physically meaningful variation with the atom type, in contrast to the radii set optimized for GB. Compared to several popular radii sets used with the original GB model, the new radii set shows better transferability between different classes of molecules.
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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.