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Bioinformatics. 2015 Sep 15;31(18):3035-42. doi: 10.1093/bioinformatics/btv302. Epub 2015 May 13.

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations.

Author information

1
Department of Biological Chemistry, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA, Department of Basic Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58203, USA and Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
2
Department of Biological Chemistry, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA, Department of Basic Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58203, USA and Department of Computer Engineering, Bogazici University, Istanbul, Turkey Department of Biological Chemistry, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA, Department of Basic Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58203, USA and Department of Computer Engineering, Bogazici University, Istanbul, Turkey.

Abstract

MOTIVATION:

G protein-coupled receptors (GPCRs) are probably the most attractive drug target membrane proteins, which constitute nearly half of drug targets in the contemporary drug discovery industry. While the majority of drug discovery studies employ existing GPCR and ligand interactions to identify new compounds, there remains a shortage of specific databases with precisely annotated GPCR-ligand associations.

RESULTS:

We have developed a new database, GLASS, which aims to provide a comprehensive, manually curated resource for experimentally validated GPCR-ligand associations. A new text-mining algorithm was proposed to collect GPCR-ligand interactions from the biomedical literature, which is then crosschecked with five primary pharmacological datasets, to enhance the coverage and accuracy of GPCR-ligand association data identifications. A special architecture has been designed to allow users for making homologous ligand search with flexible bioactivity parameters. The current database contains ∼500 000 unique entries, of which the vast majority stems from ligand associations with rhodopsin- and secretin-like receptors. The GLASS database should find its most useful application in various in silico GPCR screening and functional annotation studies.

AVAILABILITY AND IMPLEMENTATION:

The website of GLASS database is freely available at http://zhanglab.ccmb.med.umich.edu/GLASS/.

CONTACT:

zhng@umich.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25971743
PMCID:
PMC4668776
DOI:
10.1093/bioinformatics/btv302
[Indexed for MEDLINE]
Free PMC Article

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