title: BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
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 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).
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Jae-Kwan
authors.initials: JK
authors.lastname: Kim
authors.forename: Youngsong
authors.initials: Y
authors.lastname: Cho
authors.forename: Roman A
authors.initials: RA
authors.lastname: Laskowski
authors.forename: Seong Eon
authors.initials: SE
authors.lastname: Ryu
authors.forename: Kokichi
authors.initials: K
authors.lastname: Sugihara
authors.forename: Deok-Soo
authors.initials: DS
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D008968:Molecular Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000648:ultrastructure*
chemical_list: D011506:Proteins
keywords: Lee-Richards solvent accessible surface; Voronoi diagram of spheres; beta-complex; beta-shape; cavity; channel; computational geometry; geometric modeling; offset surface; quasi-triangulation; tunnel