A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states

DOI10.1007/S00285-019-01372-1zbMath1418.92042OpenAlexW2942075139WikidataQ91571846 ScholiaQ91571846MaRDI QIDQ2313961

Siwen Wang, Emil Alexov, Tania Hazra, Shan Zhao, Sheik Ahmed Ullah

Publication date: 25 July 2019

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s00285-019-01372-1

zbMATH Keywords

Poisson-Boltzmann equationelectrostatic free energyalternating direction implicit (ADI)Gaussian dielectric modelminimal molecular surfaceProtein cavity

Mathematics Subject Classification ID

PDEs in connection with biology, chemistry and other natural sciences (35Q92) Biochemistry, molecular biology (92C40) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06)

Related Items (7)

A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions ⋮ Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: a unified regularization formulation ⋮ A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces ⋮ Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential ⋮ Unnamed Item ⋮ On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary ⋮ Evolutionary de Rham-Hodge method

Uses Software

• APBS
• MIBPB
• TMSmesh
• DelPhiPKa

Cites Work

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• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• Convergence of phase-field free energy and boundary force for molecular solvation
• High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
• Quality meshing of implicit solvation models of biomolecular structures
• Progress in developing Poisson-Boltzmann equation solvers
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis
• Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules

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