Marching cubes: A high resolution 3D surface construction algorithm
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Triangulating the surface of a molecule
Discrete Applied Mathematics - Special volume on computational molecular biology
Guaranteed-quality Delaunay meshing in 3D (short version)
SCG '97 Proceedings of the thirteenth annual symposium on Computational geometry
Interval volume tetrahedrization
VIS '97 Proceedings of the 8th conference on Visualization '97
NURBS based B-rep models for macromolecules and their properties
SMA '97 Proceedings of the fourth ACM symposium on Solid modeling and applications
Using distance maps for accurate surface representation in sampled volumes
VVS '98 Proceedings of the 1998 IEEE symposium on Volume visualization
Simplifying surfaces with color and texture using quadric error metrics
Proceedings of the conference on Visualization '98
Journal of the ACM (JACM)
A Generalization of Algebraic Surface Drawing
ACM Transactions on Graphics (TOG)
Semi-regular mesh extraction from volumes
Proceedings of the conference on Visualization '00
Feature sensitive surface extraction from volume data
Proceedings of the 28th annual conference on Computer graphics and interactive techniques
Dual contouring of hermite data
Proceedings of the 29th annual conference on Computer graphics and interactive techniques
Volumetric Data Exploration Using Interval Volume
IEEE Transactions on Visualization and Computer Graphics
Dynamic maintenance and visualization of molecular surfaces
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Adaptive and quality 3D meshing from imaging data
SM '03 Proceedings of the eighth ACM symposium on Solid modeling and applications
Geometric Partial Differential Equations and Image Analysis
Geometric Partial Differential Equations and Image Analysis
Discrete surface modelling using partial differential equations
Computer Aided Geometric Design
Topologies of surfaces on molecules and their computation in O(n) time
Computer-Aided Design
Differential geometry based solvation model I: Eulerian formulation
Journal of Computational Physics
Multiscale molecular dynamics using the matched interface and boundary method
Journal of Computational Physics
Fast Molecular Solvation Energetics and Forces Computation
SIAM Journal on Scientific Computing
Adaptive skin meshes coarsening for biomolecular simulation
Computer Aided Geometric Design
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SIAM Journal on Scientific Computing
CUDA accelerated blobby molecular surface generation
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part I
Geometry guided crystal phase transition pathway search
Computer-Aided Design
3D anatomical shape atlas construction using mesh quality preserved deformable models
MeshMed'12 Proceedings of the 2012 international conference on Mesh Processing in Medical Image Analysis
3D anatomical shape atlas construction using mesh quality preserved deformable models
Computer Vision and Image Understanding
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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.