Biomolecular Object Network Databank: Difference between revisions

Revision as of 16:19, 7 May 2008

Revision as of 21:02, 1 September 2008

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==Small Molecule Interaction Database (SMID)==

The Small Molecule Interaction Database is a database containing protein ___domain-small molecule interactions. It uses a ___domain-based approach to identify ___domain families, found in the Conserved Domain Database ([[CCD]]), which interact with a [[query]] small molecule. The CCD from [[National Center for Biotechnology Information|NCBI]] amalgamates data from several different sources; [[Protein FAMilies]] (PFAM), [[Simple Modular Architecture Research Tool]] (SMART), [[Cluster of Orthologous Genes]] (COGs), and NCBI’s own curated sequences. The data in SMID is derived from the Protein Data Bank (PDB), a database of known protein crystal structures.

SMID can be queried by entering a protein GI, ___domain identifier, PDB ID or SMID ID. The results of a search provide small molecule, protein, and ___domain information for each interaction identified in the database. Interactions with non-biological contacts are normally screened out by default.