ArticleJournal of chemical theory and computation2014
Variational Implicit Solvation with Poisson-Boltzmann Theory.
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 18 papers.
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Who cites it
18 citing papers in PubMed.
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Hybrid method for representing ions in implicit solvation calculations.Computational and structural biotechnology journal · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Short solvent model for ion correlations and hydrophobic association.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.Frontiers in molecular biosciences · 2018Review
- "Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.The journal of physical chemistry. B · 2017Article
- Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.The Journal of chemical physics · 2016Article
- Numerical Treatment of Stokes Solvent Flow and Solute-Solvent Interfacial Dynamics for Nonpolar Molecules.Journal of scientific computing · 2016Article
- A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.The Journal of chemical physics · 2015Article
- Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.Journal of chemical theory and computation · 2015Article
- LS-VISM: A software package for analysis of biomolecular solvation.Journal of computational chemistry · 2015Article
- Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach.Journal of chemical theory and computation · 2015Article
- Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.The Journal of chemical physics · 2014Article
- STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.SIAM journal on applied mathematicsArticle
- DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT.SIAM journal on applied mathematicsArticle
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Authors and funding
5 authors.
Funding
Abstract
We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host-guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host-guest system. We finally discuss several issues for further improvement of VISM.
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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.