BetaVoid: Molecular voids via beta-complexes and Voronoi diagrams
- Authors
- Kim, Jae-Kwan; Cho, Youngsong; Laskowski, Roman A.; Ryu, Seong Eon; Sugihara, Kokichi; Kim, Deok-Soo
- Issue Date
- Sep-2014
- Publisher
- WILEY
- Keywords
- Lee-Richards solvent accessible surface; cavity; tunnel; channel; offset surface; Voronoi diagram of spheres; quasi-triangulation; beta-complex; beta-shape; computational geometry; geometric modeling
- Citation
- PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v.82, no.9, pp.1829 - 1849
- Indexed
- SCIE
SCOPUS
- Journal Title
- PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Volume
- 82
- Number
- 9
- Start Page
- 1829
- End Page
- 1849
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/159216
- DOI
- 10.1002/prot.24537
- ISSN
- 0887-3585
- Abstract
- 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 molecualr voids and accurate computation of their geometrical properties, surhc 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).
- Files in This Item
-
Go to Link
- Appears in
Collections - 서울 공과대학 > 서울 기계공학부 > 1. Journal Articles
- 서울 공과대학 > 서울 생명공학과 > 1. Journal Articles
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.