ArticleFrontiers in molecular biosciences2018
Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.
Article in Frontiers in molecular biosciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.Journal of computational chemistry · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Protein pJournal of chemical theory and computation · 2022Article
- Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation.ACS omega · 2022Article
- Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations.Journal of chemical theory and computation · 2021Article
- BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics.International journal of molecular sciences · 2020Article
- Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi.Journal of chemical information and modeling · 2020Article
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.Journal of computational chemistry · 2019Article
- An efficient second-order poisson-boltzmann method.Journal of computational chemistry · 2019Article
- Modeling Electrostatic Force in Protein-Protein Recognition.Frontiers in molecular biosciences · 2019Article
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6 authors.
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Abstract
Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant) from the solvent phase (high dielectric constant). Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.
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