ArticleCommunications in computational physics2013
Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.
Article in Communications in computational physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- Bluues_cplx: Electrostatics at Protein-Protein and Protein-Ligand Interfaces.Molecules (Basel, Switzerland) · 2025Article
- SiteFerret: Beyond Simple Pocket Identification in Proteins.Journal of chemical theory and computation · 2023Article
- Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment.The journal of physical chemistry. B · 2022Article
- Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics.Frontiers in molecular biosciences · 2022Article
- Antibody-Antigen Binding Interface Analysis in the Big Data Era.Frontiers in molecular biosciences · 2022Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- 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
- A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.Journal of computational chemistry · 2019Article
- NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.Bioinformatics (Oxford, England) · 2019Article
- Frontiers in biomolecular mesh generation and molecular visualization systems.Visual computing for industry, biomedicine, and art · 2018Review
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation.Journal of molecular modeling · 2015Article
- Implicit solvent methods for free energy estimation.European journal of medicinal chemistry · 2015Review
- Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.Journal of theoretical & computational chemistry · 2014Article
- Theoretical study on the allosteric regulation of an oligomeric protease from Pyrococcus horikoshii by Cl- Ion.Molecules (Basel, Switzerland) · 2014Article
- A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation.BioMed research international · 2014Article
- Multiscale geometric modeling of macromolecules II: Lagrangian representation.Journal of computational chemistry · 2013Article
- Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation.Journal of chemical theory and computation · 2013Article
- Progress in developing Poisson-Boltzmann equation solvers.Molecular based mathematical biology · 2013Article
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6 authors.
Funding
Abstract
The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the
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