Progress in developing Poisson-Boltzmann equation solvers

DOI10.2478/mlbmb-2013-0002zbMath1277.65086OpenAlexW2032579758WikidataQ30447589 ScholiaQ30447589MaRDI QIDQ2863922

Emil Alexov, Chuan Li, Marharyta Petukh, Lin Li

Publication date: 5 December 2013

Published in: Computational and Mathematical Biophysics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.2478/mlbmb-2013-0002

zbMATH Keywords

numerical techniquesPoisson-Boltzmann equationcontinuum electrostaticsdielectric constantmolecular surface

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Parallel algorithms in computer science (68W10) Biophysics (92C05) Finite difference methods for boundary value problems involving PDEs (65N06) Boundary element methods for boundary value problems involving PDEs (65N38) Computational methods for problems pertaining to biology (92-08)

Related Items (5)

Computational modeling of protein conformational changes -- application to the opening SARS-CoV-2 spike ⋮ Solving fluctuation-enhanced Poisson-Boltzmann equations ⋮ Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation ⋮ A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation ⋮ A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states

Uses Software

• NAMD
• Gromacs
• APBS
• CHARMM
• UHBD
• MIBPB
• AFMPB
• FFTSVD
• TMSmesh
• SG
• Apbsmem
• DelPhi

Cites Work

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