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BetaVoid: Molecular voids via beta‐complexes and Voronoi diagrams
Author(s) -
Kim JaeKwan,
Cho Youngsong,
Laskowski Roman A,
Ryu Seong Eon,
Sugihara Kokichi,
Kim DeokSoo
Publication year - 2014
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - Uncategorized
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24537
Subject(s) - voronoi diagram , correctness , weighted voronoi diagram , computation , benchmark (surveying) , centroidal voronoi tessellation , computer science , power diagram , algorithm , topology (electrical circuits) , theoretical computer science , mathematics , combinatorics , geometry , geodesy , geography
Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta-complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr).