Ligand-gated ion channel database (LGICdb)

Ligand-gated ion channel database (LGICdb) catalogs annotated nucleic acid and protein sequences, multiple sequence alignments, phylogenetic analyses, and available atomic coordinates for ligand-gated ion channels (LGICs), polymeric transmembrane proteins mediating rapid neurotransmitter responses, to support sequence, evolutionary, and structural research.

Key Features:

• Centralized Gene Entries: Each gene is represented by a single database entry linking sequences and annotations for its LGIC subunits.
• Annotated Sequences: Curated nucleic acid and protein sequences are provided for individual LGIC subunits.
• Multiple Sequence Alignments: Multiple sequence alignments are available to facilitate comparative studies across subunits and species.
• Phylogenetic Analyses: Phylogenetic analyses of LGIC superfamilies are provided to infer evolutionary relationships.
• Atomic Coordinates Availability: Atomic coordinates for complete subunits or subunit fragments are included when experimentally determined structures exist.

Scientific Applications:

• Neurobiology: Supports investigation of the molecular mechanisms of neurotransmission mediated by LGICs.
• Pharmacology: Informs receptor pharmacology and drug design efforts targeting LGICs.
• Molecular Genetics: Enables analysis of genetic diversity and sequence variation among LGIC genes across species.
• Evolutionary Analysis: Facilitates studies of evolutionary relationships within LGIC superfamilies using sequence and phylogenetic data.
• Structural Biology: Supports structural interpretation of receptor function using available atomic coordinates.

Methodology:

Careful curation of gene sequences and associated data from a variety of sources.