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BMC Bioinformatics. 2004 Dec 24;5:208.

A database for G proteins and their interaction with GPCRs.

Author information

  • 1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece. aelef_79@yahoo.gr

Abstract

BACKGROUND:

G protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subunits (alpha,beta,gamma). The alpha subunit of the G protein is responsible for the recognition of a given GPCR. Whereas specialised resources for GPCRs, and other groups of receptors, are already available, currently, there is no publicly available database focusing on G Proteins and containing information about their coupling specificity with their respective receptors.

DESCRIPTION:

gpDB is a publicly accessible G proteins/GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers (272 Galpha, 87 Gbeta and 59 Ggamma) and 2782 GPCRs sequences belonging to families with known coupling to G proteins. The GPCRs and the G proteins are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature searchs. The main innovation besides the classification of both G proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, references to the literature concerning the coupling specificity and the dimerization of GPCRs and the user may submit advanced queries for text search. Furthermore, we provide a pattern search tool, an interface for running BLAST against the database and interconnectivity with PRED-TMR, PRED-GPCR and TMRPres2D.

CONCLUSIONS:

The database will be very useful, for both experimentalists and bioinformaticians, for the study of G protein/GPCR interactions and for future development of predictive algorithms. It is available for academics, via a web browser at the URL: http://bioinformatics.biol.uoa.gr/gpDB.

PMID:
15619328
[PubMed - indexed for MEDLINE]
PMCID:
PMC544346
Free PMC Article
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