BetaVoid: Molecular voids via beta‐complexes and Voronoi diagrams. Issue 9 (20th March 2014)

• Record Type: Journal Article
• Authors: Kim, Jae‐Kwan; Cho, Youngsong; Laskowski, Roman A; Ryu, Seong Eon; Sugihara, Kokichi; Kim, Deok‐Soo
• Is Part Of: Proteins. Volume 82:Issue 9(2014)
• Page Start: 1829
• Page End: 1849
• Publication Date: 2014-03-20
• Subjects: Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24537
• Languages: English
• ISSNs: 0887-3585

Abstract

<abstract abstract-type="main"> <title>Abstract</title> <p>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 <bold>BetaVoid</bold> to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the <bold>BetaVoid</bold> program which is freely available at the Voronoi Diagram Research Center (<ext-link ext-link-type="uri" xlink:href="http://voronoi/hanyang.ac.kr" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://voronoi.hanyang.ac.kr</ext-link>). Proteins 2014; 82:1829–1849. © 2014 Wiley Periodicals, Inc.</p> </abstract>