Pocket extraction on proteins via the Voronoi diagram of spheres

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Title
Pocket extraction on proteins via the Voronoi diagram of spheres
Author(s)
D Kim; C H Cho; Y Cho; J Ryu; Jong Bhak; D S Kim
Bibliographic Citation
Journal of Molecular Graphics & Modelling, vol. 26, no. 7, pp. 1104-1112
Publication Year
2008
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.
Keyword
Binding siteBlending meshDockingPocketProteinProtein surfaceVoronoi diagram of atoms
ISSN
1093-3263
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.jmgm.2007.10.002
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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