BetaCavityWeb: a webserver for molecular voids and channels

Jae-Kwan Kim; Youngsong Cho; Mokwon Lee; Roman A Laskowski; Seong Eon Ryu; Kokichi Sugihara; Deok-Soo Kim

doi:10.1093/nar/gkv360

BetaCavityWeb: a webserver for molecular voids and channels

Nucleic Acids Res. 2015 Jul 1;43(W1):W413-8. doi: 10.1093/nar/gkv360. Epub 2015 Apr 22.

Authors

Jae-Kwan Kim¹, Youngsong Cho¹, Mokwon Lee², Roman A Laskowski³, Seong Eon Ryu⁴, Kokichi Sugihara⁵, Deok-Soo Kim⁶

Affiliations

¹ Vorononi Diagram Research Center, Hanyang University, Korea.
² School of Mechanical Engineering, Hanyang University, Korea.
³ European Bioinformatics Institute, Wellcome Trust Genome Campus, UK.
⁴ Department of Bioengineering, Hanyang University, Korea.
⁵ Meiji Institute for Advanced Study of Mathematical Sciences, Tokyo, Japan.
⁶ Vorononi Diagram Research Center, Hanyang University, Korea School of Mechanical Engineering, Hanyang University, Korea dskim@hanyang.ac.kr.

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).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Internet
Models, Molecular
Molecular Conformation*
Protein Conformation
Software*