김재관
2017-01-10T01:30:42Z
2017-01-10T01:30:42Z
2015-05
PLOS ONE, v. 10, Page. 1-29
1932-6203
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122787
http://hdl.handle.net/20.500.11754/25007
Structure-based virtual screening is one of the most important and common computational methods for the identification of predicted hit at the beginning of drug discovery. Pocket recognition and definition is frequently a prerequisite of structure-based virtual screening, reducing the search space of the predicted protein-ligand complex. In this paper, we present an optimal ligand shape descriptor for a pocket recognition algorithm based on the beta-shape, which is a derivative structure of the Voronoi diagram of atoms. We investigate six candidates for a shape descriptor for a ligand using statistical analysis: the minimum enclosing sphere, three measures from the principal component analysis of atoms, the van der Waals volume, and the beta-shape volume. Among them, the van der Waals volume of a ligand is the optimal shape descriptor for pocket recognition and best tunes the pocket recognition algorithm based on the beta-shape for efficient virtual screening. The performance of the proposed algorithm is verified by a benchmark test.
J-KK, C-IW, JC, and D-SK were supported by the National Research Foundation grant funded by MSIP (No. 2012R1A2A1A05026395), Republic of Korea. KL was supported by the grant (201400000002667) funded by Small and Medium Business Administration (SMBA), Republic of Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
en
PUBLIC LIBRARY SCIENCE
DRUG DISCOVERY
BINDING-SITES
VORONOI-DIAGRAM
MOLECULAR RECOGNITION
QUASI-TRIANGULATION
PROTEIN SURFACES
DOCKING
CAVITIES
INHIBITORS
COMPLEX
Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape
Article
10
10.1371/journal.pone.0122787
1-29
PLOS ONE
Kim, Jae-Kwan
Won, Chung-In
Cha, Jehyun
Lee, Kichun
Kim, Deok-Soo
2015008685
S
DIVISION OF INTERDISCIPLINARY INDUSTRIAL STUDIES[S]
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