Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jan;36(Database issue):D907-12.
doi: 10.1093/nar/gkm948. Epub 2007 Nov 5.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update

Yasushi Okuno  1 , Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, Chunlai Feng
Affiliations

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update

Yasushi Okuno et al. Nucleic Acids Res. 2008 Jan.

Abstract

G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GLIDA is a public GPCR-related Chemical Genomics database that is primarily focused on the integration of information between GPCRs and their ligands. It provides interaction data between GPCRs and their ligands, along with chemical information on the ligands, as well as biological information regarding GPCRs. These data are connected with each other in a relational database, allowing users in the field of Chemical Genomics research to easily retrieve such information from either biological or chemical starting points. GLIDA includes a variety of similarity search functions for the GPCRs and for their ligands. Thus, GLIDA can provide correlation maps linking the searched homologous GPCRs (or ligands) with their ligands (or GPCRs). By analyzing the correlation patterns between GPCRs and ligands, we can gain more detailed knowledge about their conserved molecular recognition patterns and improve drug design efforts by focusing on inferred candidates for GPCR-specific drugs. This article provides a summary of the GLIDA database and user facilities, and describes recent improvements to database design, data contents, ligand classification programs, similarity search options and graphical interfaces. GLIDA is publicly available at http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/. We hope that it will prove very useful for Chemical Genomics research and GPCR-related drug discovery.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
A screenshot of GLIDA showing linked relations among search pages (a and b), result pages (c and d), an analytical report page (e), and a binding information page (f). The analytical report page consists of a correlation map and a list resulting from a similarity search. Red and blue colors of the spots on the correlation map indicate the ligand activities of antagonists including inverse agonist and agonists including full/partial agonist, respectively.
Figure 2.
Figure 2.
A screenshot of the ligand search process on the ligand classification page. Users can search the ligands from two starting points: keyword search and cluster selection. If they have a chemical structure of their query compound, the ligand search is performed using the cluster selection tool as follows. Selecting a set of atom types (step 1) that the query compound contains, the pull-down menu of cluster selection displays the list of the only clusters that include selected atom types as the principal components (step 2). By selecting a cluster from the list, users can check the principal component's atoms on the upper right section of the page. Finally, upon clicking the search button, GLIDA displays the list of all ligands classified in the selected cluster (step 3). The ‘Atom Type TABLE’ button links the user to the page showing the cluster size and representative atom types for each cluster.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. George SR, O’Dowd BF, Lee SP. G-protein-coupled receptor oligomerization and its potential for drug discovery. Nature Rev. Drug Discov. 2002;1:808–820. - PubMed
    1. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 2003;31:294–297. - PMC - PubMed
    1. Strachan R, Ferrara G, Roth BL. Screening the receptorome: an efficient approach for drug discovery and target validation. Drug Discov. Today. 2006;11:708–716. - PubMed
    1. Foord SM, Bonner TI, Neubig RR, Rosser EM, Pin JP, Davenport AP, Spedding M, Harmar AJ. International Union of Pharmacology. XLVI. G Protein-Coupled Receptor List. Pharmacol. Rev. 2005;57:279–288. - PubMed
    1. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2007;35:12. - PMC - PubMed

Publication types