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Bioinformatics. 2011 Jun 15;27(12):1736-8. doi: 10.1093/bioinformatics/btr190. Epub 2011 Apr 19.

Signaling gateway molecule pages--a data model perspective.

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  • 1Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.

Abstract

SUMMARY:

The Signaling Gateway Molecule Pages (SGMP) database provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. A molecule page starts with astate of a native protein, without any modification and/or interactions. New states are formed with every post-translational modification or interaction with one or more proteins, small molecules or class molecules and with each change in cellular location. State transitions are caused by a combination of one or more modifications, interactions and translocations which then might be associated with one or more biological processes. In a characterized biological state, a molecule can function as one of several entities or their combinations, including channel, receptor, enzyme, transcription factor and transporter. We have also exported SGMP data to the Biological Pathway Exchange (BioPAX) and Systems Biology Markup Language (SBML) as well as in our custom XML.

AVAILABILITY:

SGMP is available at www.signaling-gateway.org/molecule.

PMID:
21505029
[PubMed - indexed for MEDLINE]
PMCID:
PMC3106186
Free PMC Article

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