ArticleJournal of chemical theory and computation2012
Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- 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
- 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
- Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists.Scientific reports · 2016Article
- 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
- 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
- Variational Implicit Solvation with Poisson-Boltzmann Theory.Journal of chemical theory and computation · 2014Article
- Heterogeneous Hydration of p53/MDM2 Complex.Journal of chemical theory and computation · 2014Article
- Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|Journal of chemical theory and computation · 2013Article
- Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation.The Journal of chemical physics · 2013Article
- Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation.Journal of chemical theory and computation · 2013Article
- Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.SIAM journal on applied mathematics · 2013Article
- Motion of a Cylindrical Dielectric Boundary.SIAM journal on applied mathematics · 2013Article
- Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force.Nonlinearity · 2011Article
- Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach.SIAM journal on applied mathematics · 2011Article
- STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.SIAM journal on applied mathematicsArticle
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6 authors.
Funding
Abstract
Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute-solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective boundary force and use it as the "normal velocity" in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach.
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