Small Molecule Pathway Database
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The Small Molecule Pathway Database (SMPDB)[1] is a unique bioinformatics database that presents visual and interactive displays of over 350 small molecule pathways from the human body. Over two thirds of the pathways in the SMPDB are not available in any other pathway database. Researchers in proteomics, transcriptomics, metabolomics, and systems biology can use this database for pathway discovery and elucidation. SMPDB includes the following pathway types: drug-action pathways, metabolic disease pathways, human metabolic pathways, and metabolite-signaling pathways. The SMPDB pathways are very detailed, fully searchable, and contain hyperlinks to the HMDB, DrugBank, and UniProt.[2]
Users can browse the SMPDB or search its contents by text searching, sequence searching, or chemical structure searching. More powerful queries are also possible including searching with lists of gene or protein names, drug names, metabolite names, GenBank IDs, Swiss-Prot IDs, Agilent or or Affymetrix microarray IDs. Much of the SMPDB's content can be downloaded[3] [4] including its descriptions, tables, images, and image maps.[5]
SMPDB is part of a suite of metabolomics databases that also includes HMDB, DrugBank, and T3DB. While DrugBank includes information on 6707 drugs and 4228 non-redundant drug targets, enzymes, transporters, and carriers, HMDB houses over 7900 small molecule metabolites found in the human body. The suite is complemented by T3DB with its over 2900 toxins and over 1300 corresponding toxin targets.
References
- ^ Frolkis, A (2010 Jan). "SMPDB: The Small Molecule Pathway Database". Nucleic acids research. 38 (Database issue): D480-7. PMID 19948758.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ "SMPDB". Retrieved 11 January 2012.
- ^ "SMPDB: Data Downloads". Retrieved 11 January 2012.
- ^ "SMPDB: Image Downloads". Retrieved 11 January 2012.
- ^ "SMPDB". Retrieved 11 January 2012.