Alpha Shapes and Proteins

Author

Winter, Pawel ; Sterner, Henrik ; Sterner, Peter

Author_Institution

Dept. of Comput. Sci., Univ. of Copenhagen, Copenhagen, Denmark

fYear

2009

fDate

23-26 June 2009

Firstpage

217

Lastpage

224

Abstract

We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicial complexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation.

Keywords

biology computing; filtration; parallel algorithms; proteins; beta shapes; filtrations; geometrical constructs; parallel algorithm; protein-related problems; proteins; simplicial complexes; weighted alpha shapes; Amino acids; Biological system modeling; Computational biology; Computational geometry; Computational modeling; Filtration; Mathematical model; Proteins; Shape; Solvents; alpha complex; beta complex; beta shape; delaunay complex; filtration; power diagram; protein; voronoi diagram;

fLanguage

English

Publisher

ieee

Conference_Titel

Voronoi Diagrams, 2009. ISVD '09. Sixth International Symposium on

Conference_Location

Copenhagen

Print_ISBN

978-1-4244-4769-5

Electronic_ISBN

978-0-7695-3781-8

Type

conf

DOI

10.1109/ISVD.2009.25

Filename

5362341