Segmenting molecular surfaces

Authors:
Vijay Natarajan;Yusu Wang;Peer-Timo Bremer;Valerio Pascucci;Bernd Hamann
Affiliations:
Institute for Data Analysis and Visualization, University of California, Davis, USA;Department of Computer Science and Engineering, The Ohio State University, USA;Department of Computer Science, University of Illinois, Urbana-Champaign, USA;Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, USA;Institute for Data Analysis and Visualization, University of California, Davis, USA and Department of Computer Science, University of California, Davis, USA
Venue:
Computer Aided Geometric Design - Special issue: Applications of geometric modeling in the life sciences
Year:
2006

Citing 10
Cited 6

Topology matching for fully automatic similarity estimation of 3D shapes

Proceedings of the 28th annual conference on Computer graphics and interactive techniques
Partitioning 3D Surface Meshes Using Watershed Segmentation

IEEE Transactions on Visualization and Computer Graphics
Hierarchical isosurface segmentation based on discrete curvature

VISSYM '03 Proceedings of the symposium on Data visualisation 2003
Dynamic maintenance and visualization of molecular surfaces

Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Molecular shape analysis based upon the morse-smale complex and the connolly function

Proceedings of the nineteenth annual symposium on Computational geometry
Morse-smale complexes for piecewise linear 3-manifolds

Proceedings of the nineteenth annual symposium on Computational geometry
A Formulation of Boundary Mesh Segmentation

3DPVT '04 Proceedings of the 3D Data Processing, Visualization, and Transmission, 2nd International Symposium
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes

VIS '04 Proceedings of the conference on Visualization '04
Volumetric Data Analysis using Morse-Smale Complexes

SMI '05 Proceedings of the International Conference on Shape Modeling and Applications 2005
A topological hierarchy for functions on triangulated surfaces

IEEE Transactions on Visualization and Computer Graphics

A Morse-Theory Based Method for Segmentation of Triangulated Freeform Surfaces

ISVC '09 Proceedings of the 5th International Symposium on Advances in Visual Computing: Part II
Separatrix persistence: extraction of salient edges on surfaces using topological methods

SGP '09 Proceedings of the Symposium on Geometry Processing
Topologies of surfaces on molecules and their computation in O(n) time

Computer-Aided Design
Short Communication to SMI 2011: Surface feature based mesh segmentation

Computers and Graphics
Fitting spheres to electron density

Proceedings of the twenty-seventh annual symposium on Computational geometry
Interactive extraction and tracking of biomolecular surface features

EuroVis '13 Proceedings of the 15th Eurographics Conference on Visualization

Quantified Score

Hi-index	0.00

Visualization

Abstract

This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of the scalar function. The segmentation is obtained by associating segments with local minima/maxima. Controlled simplification of the function merges segments resulting in a hierarchical segmentation of the molecular surface. This segmentation is used to identify rigid components of protein molecules and to study the role of cavities and protrusions in protein-protein interactions.