A boundary element formulation of protein electrostatics with explicit ions

DOI10.1016/J.JCP.2006.09.011MaRDI QIDQ876460zbMATH OpenOpenAlexFDO

Authors Weidong Xin, André H. Juffer

Publication date 18 April 2007

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2006.09.011

zbMATH Keywords

electrostaticsboundary element methodcomputer simulationpotential of mean forceproteincoarse-grained modelexplicit ionsionic strength

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biological applications of optics and electromagnetic theory (78A70) Boundary element methods for boundary value problems involving PDEs (65N38) Biophysics (92C05)

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Cites work

• scientific article; zbMATH DE number 4044987 (Why is no real title available?)
• scientific article; zbMATH DE number 46777 (Why is no real title available?)
• A simulation method of combinding boundary element method with generalized Langevin dynamics
• Angular Monte Carlo integration using quaternion parameters: A spherical reference potential for \(CC|_ 4\)
• Numerical recipes in C++. The art of scientific computing
• The Extent of Anisotropic Interactions Between Protein Molecules in Electrolyte Solutions
• The electric potential of a macromolecule in a solvent: A fundamental approach

Cited in

(13)

• Continuum electrostatics for ionic solutions with non-uniform ionic sizes
• Dielectric properties of proteins from simulations: Tools and techniques
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• A novel approach to computer simulations of protein-protein complex formation
• ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
• Salt dependent association of novel mutants of TATA-binding proteins to DNA: predictions from theory and experiments
• Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
• A Boundary Integral Formulation for Nonlocal Electrostatics
• Multiscale models and approximation algorithms for protein electrostatics
• A rapid boundary integral equation technique for protein electrostatics
• A new boundary integral equation for molecular electrostatics with charges over whole space
• Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Describes a project that uses

Uses Software

• VMD
• APBS
• Gromacs

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