Abstract
In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasi-triangulation which is the topological dual of the Voronoi diagram. Then, we compute a β-complex from the quasi-triangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a β-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a β-shape for a particular β consisting of k simplices can be located in O(log m + k) time in the worst case from the simplicies in the β-complex sorted according to the interval values.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Lee, B., Richards, F.M.: The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology 55, 379–400 (1971)
Richards, F.M.: Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering 6, 151–176 (1977)
Connolly, M.L.: Analytical molecular surface calculation. Journal of Applied Crystallography 16, 548–558 (1983)
Connolly, M.L.: Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709–713 (1983)
Edelsbrunner, H., Mücke, E.P.: Three-dimensional alpha shapes. ACM Transactions on Graphics 13(1), 43–72 (1994)
Kim, D.S., Kim, D., Sugihara, K.: Voronoi diagram of a circle set from Voronoi diagram of a point set: I. topology. Computer Aided Geometric Design 18, 541–562 (2001)
Kim, D.S., Kim, D., Sugihara, K.: Voronoi diagram of a circle set from Voronoi diagram of a point set: II. geometry. Computer Aided Geometric Design 18, 563–585 (2001)
Edelsbrunner, H.: Weighted alpha shapes. Technical Report UIUCDCS-R-92-1760, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL (1992)
Edelsbrunner, H., Facello, M., Liang, J.: On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics 88, 83–102 (1998)
Liang, J., Edelsbrunner, H., Woodward, C.: Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science 7, 1884–1897 (1998)
Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., Subramaniam, S.: Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. PROTEINS: Structure, Function, and Genetics 33, 1–17 (1998)
Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., Subramaniam, S.: Analytical shape computation of macromolecules: II. inaccessible cavities in proteins. PROTEINS: Structure, Function, and Genetics 33, 18–29 (1998)
(RCSB Protein Data Bank Homepage), http://www.rcsb.org/pdb/
Kim, D.S., Cho, Y., Kim, D.: Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Computer-Aided Design 37(13), 1412–1424 (2005)
Kim, D.S., Cho, Y., Kim, D., Cho, C.H.: Protein sructure analysis using Euclidean Voronoi diagram of atoms. In: Proceedings of the International Workshop on Biometric Technologies (BT 2004), pp. 125–129 (2004)
Kim, D.S., Cho, Y., Kim, D., Kim, S., Bhak, J., Lee, S.H.: Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis. In: Proceedings of the 1st International Symposium on Voronoi Diagrams in Science and Engineering (VD 2004), pp. 137–144 (2004)
Cho, Y., Kim, D., Kim, D.S.: Topology representation for the Voronoi diagram of 3D spheres. International Journal of CAD/CAM 5(3) (2005) (in press)
Kim, D.-S., Kim, D., Cho, Y., Sugihara, K.: Quasi-triangulation and interworld data struction in three dimensions. Computer-Aided Design (2005) (submitted)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Seo, J., Kim, D., Cho, CH., Kim, DS. (2006). A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis. In: Gavrilova, M., et al. Computational Science and Its Applications - ICCSA 2006. ICCSA 2006. Lecture Notes in Computer Science, vol 3980. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11751540_12
Download citation
DOI: https://doi.org/10.1007/11751540_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-34070-6
Online ISBN: 978-3-540-34071-3
eBook Packages: Computer ScienceComputer Science (R0)