SDPBS web server for calculation of electrostatics of ionic solvated biomolecules

DOI10.1515/mlbmb-2015-0011zbMath1347.92025OpenAlexW2581213389MaRDI QIDQ326615

Zeyun Yu, Dexuan Xie, Jinyong Ying, Yi Jiang, Yang Xie

Publication date: 12 October 2016

Published in: Molecular Based Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1515/mlbmb-2015-0011

zbMATH Keywords

finite element methodcomputer graphicsPoisson-Boltzmann equationelectrostatic potentialinteractive visualization

Mathematics Subject Classification ID

Computer graphics; computational geometry (digital and algorithmic aspects) (68U05) Biochemistry, molecular biology (92C40) Mathematical aspects of software engineering (specification, verification, metrics, requirements, etc.) (68N30)

Related Items (6)

On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics ⋮ A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule ⋮ A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models ⋮ A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules ⋮ A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference ⋮ SDPBS

Uses Software

• PETSc
• FEniCS
• APBS
• ParaView
• MIBPB
• PyMOL
• PDB2PQR
• PBEQ-Solver
• DelPhi Web Server
• TABI
• VMD
• tabipb

Cites Work

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• A Fast Solver for a Nonlocal Dielectric Continuum Model
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• DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes
• Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications

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