title: BetaCavityWeb: a webserver for molecular voids and channels.
abstract: Molecular cavities, which include voids and channels, are critical for molecular function. We present a webserver, BetaCavityWeb, which computes these cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex. The correctness of the computed result and computational efficiency are both mathematically guaranteed. BetaCavityWeb is freely accessible at the Voronoi Diagram Research Center (VDRC) (http://voronoi.hanyang.ac.kr/betacavityweb).
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Jae-Kwan
authors.initials: JK
authors.lastname: Kim
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Youngsong
authors.initials: Y
authors.lastname: Cho
authors.affiliation: School of Mechanical Engineering, Hanyang University, Korea.
authors.forename: Mokwon
authors.initials: M
authors.lastname: Lee
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, UK.
authors.forename: Roman A
authors.initials: RA
authors.lastname: Laskowski
authors.affiliation: Department of Bioengineering, Hanyang University, Korea.
authors.forename: Seong Eon
authors.initials: SE
authors.lastname: Ryu
authors.affiliation: Meiji Institute for Advanced Study of Mathematical Sciences, Tokyo, Japan.
authors.forename: Kokichi
authors.initials: K
authors.lastname: Sugihara
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea School of Mechanical Engineering, Hanyang University, Korea dskim@hanyang.ac.kr.
authors.forename: Deok-Soo
authors.initials: DS
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D012984:Software