Recognition of docking sites on a protein using beta-shape based on Voronoi diagram of atoms
- Authors
- Kim, Deok-Soo; Cho, Cheol-Hyung; Kim, Donguk; Cho, Youngsong
- Issue Date
- May-2006
- Publisher
- ELSEVIER SCI LTD
- Keywords
- pocket; binding sites; docking; Voronoi diagram of spheres; beta-shape; protein interaction; drug design
- Citation
- COMPUTER-AIDED DESIGN, v.38, no.5, pp.431 - 443
- Indexed
- SCIE
SCOPUS
- Journal Title
- COMPUTER-AIDED DESIGN
- Volume
- 38
- Number
- 5
- Start Page
- 431
- End Page
- 443
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/181509
- DOI
- 10.1016/j.cad.2005.11.008
- ISSN
- 0010-4485
- Abstract
- A protein consists of atoms. Given a protein, the automatic recognition of depressed regions on the surface of the protein, often called docking sites or pockets, is important for the analysis of interaction between a protein and a ligand and facilitates fast development of new drugs. Presented in this paper is a geometric approach for the detection of docking sites using beta-shape which is based on the Voronoi diagram for atoms in Euclidean distance metric. We first propose a geometric construct called a beta-shape which represents the proximity among atoms on the surface of a protein. Then, using the beta-shape, which takes the size differences among different atoms into account, we present an algorithm to extract the pockets for the possible docking site on the surface of a protein.
- Files in This Item
-
Go to Link
- Appears in
Collections - 서울 공과대학 > 서울 기계공학부 > 1. Journal Articles
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.