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Ligand-Gated Ion Channel Database

Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

URL: http://www.ebi.ac.uk/compneur-srv/LGICdb/

Resource ID: nif-0000-00037     Resource Type: Resource     Version: Latest Version

Keywords

equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane

Comment

Access: Open
Reuse: Open- http://www.ebi.ac.uk/compneur-srv/LGICdb/FAQ.php for information
Start date: 1994
Type: Disciplinary
Deposit: Closed
(info provided by re3data.org)

Listed By

re3data.org

Publication Link

http://lenoverelab.org/perso/lenov/PUBLIS/Lenov1999a.pdf

Abbreviation

LGICdb

Synonyms

LGIC Database

Parent Organization

Funding Information

College of France; Paris; France, Centre National de la Recherche Scientifique, European Union, Biotech and Biomed contracts, French Ministry of Higher Education and Research, Institut Pasteur,

Additional Resource Types

database

Supercategory

Resource

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 5 years ago by Anonymous

LGICdb: a manually curated sequence database after the genomes.

  • Donizelli M
  • Nucleic Acids Res.
  • 2006 1

Ligand-gated ion channels form transmembrane ionic pores controlled by the binding of chemicals. The LGICdb aims to be a non-redundant, manually curated resource offering access to the large number of subunits composing extracellularly activated ligand-gated ion channels, such as nicotinic, ATP, GABA and glutamate ionotropic receptors. Composed of more than 500 human curated entries, the XML native database has been relocated in 2004 to the EBI. Its facilities have been enhanced with a new search system, customized multiple sequence alignments and manipulation of protein structures (http://www.ebi.ac.uk/compneur-srv/LGICdb/). Despite the vast improvement of general sequence resources, the LGICdb still provide sequences unavailable elsewhere.

LGICdb: the ligand-gated ion channel database.

  • Le Novère N
  • Nucleic Acids Res.
  • 2001 1

Ligand-Gated Ion Channels (LGIC) are polymeric transmembrane proteins involved in the fast response to numerous neurotransmitters. All these receptors are formed by homologous subunits and the last two decades revealed an unexpected wealth of genes coding for these subunits. The Ligand-Gated Ion Channel database (LGICdb) has been developed to handle this increasing amount of data. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences. The repository is carefully structured and the entries can be retrieved by various criteria. In addition to the sequences, the LGICdb provides multiple sequence alignments, phylogenetic analyses and atomic coordinates when available. The database is accessible via the World Wide Web (http://www.pasteur.fr/recherche/banques/LGIC /LGIC.html), where it is continuously updated. The version 16 (September 2000) available for download contained 333 entries covering 34 species.