Geometry-guided computation of 3D electrostatics for large biomolecules

DOI10.1016/J.CAGD.2006.04.003MaRDI QIDQ2506965zbMATH OpenOpenAlexFDO

Authors Xuejun Hao, Amitabh Varshney

Publication date 10 October 2006

Published in Computer Aided Geometric Design (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.cagd.2006.04.003

zbMATH Keywords

finite difference methodsiso-surface generationlevel-of-detail of hierarchyPoisson-Boltzmann equationscalar fieldtetrahedron decomposition

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Biophysics (92C05)

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• An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations

Cites work

• A 3-D refinement algorithm suitable for adaptive and multi-grid techniques
• Dynamic maintenance and visualization of molecular surfaces.
• scientific article; zbMATH DE number 3186688 (Why is no real title available?)
• Local Bisection Refinement for N-Simplicial Grids Generated by Reflection
• Symbolic local refinement of tetrahedral grids
• Triangulating the surface of a molecule

Cited in

(11)

• Efficient calculation of fully resolved electrostatics around large biomolecules
• Computing electrostatic binding energy with the TABI Poisson-Boltzmann solver
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• Computational electrostatics for biological applications. Geometric and numerical approaches to the description of electrostatic interaction between macromolecules. Proceedings of the CEBA international meeting, Genova, Italy, July 1--3, 2013
• Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
• The geometry behind numerical solvers of the Poisson-Boltzmann equation
• Geometric and electrostatic modeling using molecular rigidity functions
• DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• Efficient computational algorithms for fast electrostatics and molecular docking
• Differential geometry based solvation model. I: Eulerian formulation

Describes a project that uses

Uses Software

• APBS
• VMD

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