Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code

DOI10.1016/j.cpc.2015.12.019zbMath1348.92008arXiv1506.03745OpenAlexW589997611WikidataQ108784881 ScholiaQ108784881MaRDI QIDQ339374

Lorena A. Barba, Christopher D. Cooper

Publication date: 10 November 2016

Published in: Computer Physics Communications (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1506.03745

zbMATH Keywords

boundary element methodPoisson-Boltzmanntreecodebiomolecular electrostaticsimplicit solventprotein surface interaction

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Biophysics (92C05) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Computational methods for problems pertaining to biology (92-08) Electro- and magnetostatics (78A30)

Related Items (1)

Effective electrostatic interactions between two overall neutral surfaces with quenched charge heterogeneity over atomic length scale

Uses Software

• CUDA
• PDB2PQR
• Python
• PyGBe
• TABI
• GitHub
• tabipb

Cites Work

• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• A Cartesian treecode for screened Coulomb interactions
• The electric potential of a macromolecule in a solvent: A fundamental approach
• An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics
• A fast algorithm for particle simulations
• tabipb
• Unnamed Item

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