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BMC Bioinformatics

, 5:208

First Online: 24 December 2004Received: 30 July 2004Accepted: 24 December 2004

Abstract

BackgroundG 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 α,β,γ. The α 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.

DescriptiongpDB is a publicly accessible G proteins-GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers 272 Gα, 87 Gβ and 59 Gγ 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 α 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.

ConclusionsThe 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

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-208 contains supplementary material, which is available to authorized users.

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Autor: Antigoni L Elefsinioti - Pantelis G Bagos - Ioannis C Spyropoulos - Stavros J Hamodrakas

Fuente: https://link.springer.com/







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