Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis

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Title
Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis
Author(s)
D S Kim; Y Cho; D Kim; Sang Soo Kim; Jong Bhak; Sung Hoon Lee
Bibliographic Citation
Japan Journal of Industrial and Applied Mathematics, vol. 22, no. 2, pp. 251-265
Publication Year
2005
Abstract
Despite its many important applications in various disciplines in sciences and engineering, the Euclidean Voronoi diagram for spheres in 3D space has not been studied as much as it deserves. In this paper, we present an algorithm to compute a Euclidean Voronoi diagram for 3D spheres and show how the diagram can be used in the analysis of protein structures. Given an initial Voronoi vertex, the presented edge-tracing algorithm follows Voronoi edges until the construction is completed in O(mn) time in the worst-case, where m and n are the numbers of edges and spheres, respectively. Once a Voronoi diagram for 3D atoms of a protein is computed, it is shown that the diagram can be used to efficiently and precisely analyze the spatial structure of the protein. It turns out that this capability of a Voronoi diagram can be crucial to solving several important problems remaining to be solved in structural biology.
Keyword
edge-tracingeuclidean voronoi diagramsprotein structure
ISSN
0916-7005
Publisher
Springer
DOI
http://dx.doi.org/10.1007/BF03167441
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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