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, 27 (12), 1736-8

Signaling Gateway Molecule Pages--A Data Model Perspective

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Signaling Gateway Molecule Pages--A Data Model Perspective

Ashok Reddy Dinasarapu et al. Bioinformatics.

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.

Figures

Fig. 1.
Fig. 1.
Schematic representation of some states. A new state is formed (i) with a native protein itself (ii) with covalent modification(s) (iii) with binding to small molecule (iv–ix) with binding to one or more other proteins, small molecules, modifications, etc. and (x–xiii) above changes with a class molecule. Molecule, molecule page protein; m, covalent modification; protein, other binding protein; loc, cellular location; sm, small molecule.

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