Pocket extraction on proteins via the Voronoi diagram of spheres
- Authors
- Kim, Donguk; Cho, Cheol-Hyung; Cho, Youngsong; Ryu, Joonghyun; Bhak, Jonghwa; Kim, Deok-Soo
- Issue Date
- Apr-2008
- Publisher
- ELSEVIER SCIENCE INC
- Keywords
- Voronoi diagram of atoms; protein; pocket; binding site; docking; protein surface; blending mesh
- Citation
- JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v.26, no.7, pp.1104 - 1112
- Indexed
- SCIE
SCOPUS
- Journal Title
- JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Volume
- 26
- Number
- 7
- Start Page
- 1104
- End Page
- 1112
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/178786
- DOI
- 10.1016/j.jmgm.2007.10.002
- ISSN
- 1093-3263
- Abstract
- Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes.
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