The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience.

Multiple comparisons of receptor sequences, or receptor subunit sequences, has proved to be an invaluable tool in modern pharmacological investigations. Although of outstanding importance, general sequence databases suffer from several imperfections due to their size and their non-specificity. Room therefore exists for expert-maintained databases of restricted focus, where knowledge of the research field helps to filter the huge amount of data generated. Accordingly, neuroscientists have designed databases covering several types of proteins, in particular receptors for neurotransmitters. Ligand-gated ion channels are oligomeric transmembrane proteins involved in the fast response to neurotransmitters. All these receptors are formed by the assembly of homologous subunits, and an unexpected wealth of genes coding for these subunits has been revealed during the last two decades. The Ligand Gated Ion Channel database (LGICdb) has been developed to handle this growing body of information. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences.

[1]  B Rost,et al.  Bridging the protein sequence-structure gap by structure predictions. , 1996, Annual review of biophysics and biomolecular structure.

[2]  Jean-Pierre Toutant,et al.  aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server , 1998, Nucleic Acids Res..

[3]  Rodrigo Lopez,et al.  The EMBL Nucleotide Sequence Database , 1999, Nucleic Acids Res..

[4]  Nicolas Le Novère,et al.  The Ligand Gated Ion Channel Database , 1999, Nucleic Acids Res..

[5]  Jean-Luc Galzi,et al.  Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic , 1992, Nature.

[6]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams , 2000, Nucleic Acids Res..

[7]  Hong Xue,et al.  GABAagent: a system for integrating data on GABA receptors , 2000, Bioinform..

[8]  Gert Vriend,et al.  GPCRDB information system for G protein-coupled receptors , 2003, Nucleic Acids Res..

[9]  Eric Gouaux,et al.  Functional characterization of a potassium-selective prokaryotic glutamate receptor , 1999, Nature.

[10]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[11]  J. Changeux,et al.  The multiple phenotypes of allosteric receptor mutants. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[12]  E A Barnard,et al.  The transmitter-gated channels: a range of receptor types and structures. , 1996, Trends in pharmacological sciences.

[13]  Peter B. McGarvey,et al.  The Protein Information Resource (PIR) , 2000, Nucleic Acids Res..

[14]  Nicolas Le Novère,et al.  LGICdb: the ligand-gated ion channel database , 2001, Nucleic Acids Res..

[15]  C. Malbon,et al.  Physiological regulation of G protein-linked signaling. , 1999, Physiological reviews.

[16]  Jean-Luc Galzi,et al.  Neurotransmitter-gated ion channels as unconventional allosteric proteins , 1994 .

[17]  Catherine Letondal,et al.  A Web interface generator for molecular biology programs in Unix , 2001, Bioinform..

[18]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Kotoko Nakata,et al.  Development of the receptor database (RDB): application to the endocrine disruptor problem , 1999, Bioinform..

[20]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[21]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[22]  Øyvind Edvardsen,et al.  A database of mutants and effects of site‐directed mutagenesis experiments on G protein‐coupled receptors , 1996, Proteins.

[23]  J. Changeux,et al.  Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation. , 1999, Biophysical journal.

[24]  A M Lesk,et al.  CASP2: Report on ab initio predictions , 1997, Proteins.

[25]  R. Dingledine,et al.  The glutamate receptor ion channels. , 1999, Pharmacological reviews.

[26]  Kolakowski Lf.  GCRDB: A G-PROTEIN-COUPLED RECEPTOR DATABASE , 1994 .

[27]  T. Bonner,et al.  Definition of pharmacological receptors. , 1992, Pharmacological reviews.

[28]  Chris Sander,et al.  MView: a web-compatible database search or multiple alignment viewer , 1998, Bioinform..

[29]  J. Changeux,et al.  Critical Elements Determining Diversity in Agonist Binding and Desensitization of Neuronal Nicotinic Acetylcholine Receptors , 1998, The Journal of Neuroscience.

[30]  George G. Lunt,et al.  Evolutionary history of the ligand-gated ion-channel superfamily of receptors , 1995, Trends in Neurosciences.

[31]  Walter Gilbert,et al.  Towards a paradigm shift in biology , 1991, Nature.

[32]  A. Nicke,et al.  P2X1 and P2X3 receptors form stable trimers: a novel structural motif of ligand‐gated ion channels , 1998, The EMBO journal.

[33]  J. Vincent,et al.  Early Emergence of Three Dopamine D1 Receptor Subtypes in Vertebrates , 1997, The Journal of Biological Chemistry.

[34]  Perry L. Miller,et al.  Olfactory Receptor Database: a database of the largest eukaryotic gene family , 1999, Nucleic Acids Res..