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- Bhak, Jong
- KOrean GenomIcs Center
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Pocket extraction on proteins via the Voronoi diagram of spheres
- Alternative Title
- Pocket extraction on proteins via the Voronoi diagram of spheres.
- Author(s)
- Kim, Donguk, Cho, Cheol-Hyung, Cho, Youngsong, Ryu, Joonghyun, Bhak, Jong Hwa, Kim, Deok-Soo
- Issued Date
- 2008-04
- Citation
- JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v.26, no.7, pp.1104 - 1112
- 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. (c) 2007 Elsevier Inc. All rights reserved
- Publisher
- ELSEVIER SCIENCE INC
- ISSN
- 1093-3263
- Keyword (Author)
- Voronoi diagram of atoms, protein, pocket, binding site, docking, protein surface, blending mesh
- Keyword
- BINDING SITES, 3D SPHERES, SURFACES, CAVITIES, VOLUME, SPACE, ATOMS, POLYHEDRA, DENSITY, DOCKING
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