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. 2008 Apr;26(7):1104-12.
doi: 10.1016/j.jmgm.2007.10.002. Epub 2007 Oct 7.

Pocket extraction on proteins via the Voronoi diagram of spheres

Donguk Kim  1 , Cheol-Hyung Cho, Youngsong Cho, Joonghyun Ryu, Jonghwa Bhak, Deok-Soo Kim
Affiliations

Pocket extraction on proteins via the Voronoi diagram of spheres

Donguk Kim et al. J Mol Graph Model. 2008 Apr.

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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