ArticleComputer aided geometric design2006
Quality Meshing of Implicit Solvation Models of Biomolecular Structures.
Article in Computer aided geometric design, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual.Journal of chemical information and modeling · 2025Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- Frontiers in biomolecular mesh generation and molecular visualization systems.Visual computing for industry, biomedicine, and art · 2018Review
- GPU-based detection of protein cavities using Gaussian surfaces.BMC bioinformatics · 2017Article
- Tissue-scale, personalized modeling and simulation of prostate cancer growth.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Object-oriented Persistent Homology.Journal of computational physics · 2016Article
- Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation.Journal of molecular modeling · 2015Article
- On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.Journal of theoretical & computational chemistry · 2014Article
- Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.Molecular based mathematical biology · 2013Article
- Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.Communications in computational physics · 2013Article
- High-order fractional partial differential equation transform for molecular surface construction.Molecular based mathematical biology · 2013Article
- Feature-preserving surface mesh smoothing via suboptimal Delaunay triangulation.Graphical models · 2013Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Biomolecular surface construction by PDE transform.International journal for numerical methods in biomedical engineering · 2012Article
- ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION.Communications in computational physics · 2012Article
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- Quality Mesh Smoothing via Local Surface Fitting and Optimum Projection.Graphical models · 2011Article
- Adaptive Skin Meshes Coarsening for Biomolecular Simulation.Computer aided geometric design · 2011Article
- Multiscale molecular dynamics using the matched interface and boundary method.Journal of computational physics · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
This paper describes a comprehensive approach to construct quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). First, a smooth volumetric electron density map is constructed from atomic data using weighted Gaussian isotropic kernel functions and a two-level clustering technique. This enables the selection of a smooth implicit solvation surface approximation to the Lee-Richards molecular surface. Next, a modified dual contouring method is used to extract triangular meshes for the surface, and tetrahedral meshes for the volume inside or outside the molecule within a bounding sphere/box of influence. Finally, geometric flow techniques are used to improve the surface and volume mesh quality. Several examples are presented, including generated meshes for biomolecules that have been successfully used in finite element simulations involving solvation energetics and binding rate constants.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.