Real-time triangulation of molecular surfaces

Authors:
Joonghyun Ryu;Rhohun Park;Jeongyeon Seo;Chongmin Kim;Hyun Chan Lee;Deok-Soo Kim
Affiliations:
Voronoi Diagram Research Center, Hanyang University, Seoul, Korea;Voronoi Diagram Research Center, Hanyang University, Seoul, Korea;Department of Industrial Engineering, Hanyang University, Seoul, Korea;Department of Industrial Engineering, Hanyang University, Seoul, Korea;Department of Industrial Engineering, Hongik University, Seoul, Korea;Department of Industrial Engineering, Hanyang University, Seoul, Korea
Venue:
ICCSA'07 Proceedings of the 2007 international conference on Computational science and its applications - Volume Part I
Year:
2007

Citing 10
Cited 1

Three-dimensional alpha shapes

ACM Transactions on Graphics (TOG)
Spheres, molecules, and hidden surface removal

SCG '94 Proceedings of the tenth annual symposium on Computational geometry
NURBS based B-rep models for macromolecules and their properties

SMA '97 Proceedings of the fourth ACM symposium on Solid modeling and applications
Computing Smooth Molecular Surfaces

IEEE Computer Graphics and Applications
Dynamic maintenance and visualization of molecular surfaces

Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Guaranteed Quality Triangulation of Molecular Skin Surfaces

VIS '04 Proceedings of the conference on Visualization '04
\beta-shape Based Computation of Blending Surfaces on a Molecule

ISVD '07 Proceedings of the 4th International Symposium on Voronoi Diagrams in Science and Engineering
Molecular surfaces on proteins via beta shapes

Computer-Aided Design
Region-expansion for the Voronoi diagram of 3D spheres

Computer-Aided Design
Euclidean Voronoi diagram of 3D balls and its computation via tracing edges

Computer-Aided Design

Special Section on CAD/Graphics 2013: Triangulation of molecular surfaces based on extracting surface atoms

Computers and Graphics

Quantified Score

Hi-index	0.00

Visualization

Abstract

Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defined with respect to a probe approximating a solvent molecule. This paper presents an efficient, as efficient as the realtime, algorithm to triangulate the blending surfaces which is the most critical subset of a molecular surface. For the quick evaluation of points on the surface, the proposed algorithm uses masks which are similar in their concepts to those in subdivision surfaces. More fundamentally, the proposed algorithm takes advantage of the concise representation of topology among atoms stored in the β-shape which is indeed used in the computation of the blending surface itself. Given blending surfaces and the corresponding β-shape, the proposed algorithm triangulates the blending surfaces in O(c ċ m) time in the worst case, where m is the number of boundary atoms in the protein and c is the number of point evaluations on a patch in the blending surface.