ArticleJournal of theoretical & computational chemistry2014
On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.
Article in Journal of theoretical & computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 40 citations in OpenAlex.
- On generalizing the induced surface charge method to heterogeneous Poisson-Boltzmann models for electrostatic free energy calculation.Journal of computational physics · 2026Article
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential.Journal of computational physics · 2024Article
- PyUUL provides an interface between biological structures and deep learning algorithms.Nature communications · 2022Article
- AweGNN: Auto-parametrized weighted element-specific graph neural networks for molecules.Computers in biology and medicine · 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
- A computational model of ESAT-6 complex in membrane.Journal of theoretical & computational chemistry · 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
- Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.Computational and structural biotechnology journal · 2020Review
- 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
- Modeling Electrostatic Force in Protein-Protein Recognition.Frontiers in molecular biosciences · 2019Article
- Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.Bioinformatics (Oxford, England) · 2018Article
- 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
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.Journal of computational chemistry · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions.Scientific reports · 2016Article
- Electrostatic effects on the folding stability of FKBP12.Protein engineering, design & selection : PEDS · 2016Article
- Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.Scientific reports · 2016Article
- Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.Methods in enzymology · 2016Review
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3 authors at 1 institution in 1 country.
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Abstract
Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute-water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.
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