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COMe - Co-Ordination of Metals etc.


NAR Molecular Biology Database Collection entry number 438
Degtyarenko, K., Contrino, S.
EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Database Description

COMe (Co-Ordination of Metals etc.) represents the classification of bioinorganic proteins. COMe consists of three types of entries: "bioinorganic motif", "molecule", and "complex protein"; each entry is assigned a unique identifier. A bioinorganic motif (BIM) consists of at least one centre (metal atom, inorganic cluster, organic molecule) and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional strings and two-dimensional diagrams. A molecule (MOL) represents any molecular entity ("small molecule") which, in complex with polypeptide(s), forms a functional protein. A complex protein (PRX) entry may refer to the functional protein as well as separate protein domains and subunits. The main classes of complex proteins in COMe are (i) metalloproteins, (ii) organic prosthetic group proteins and (iii) modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.flymine.org/come/.

References

Degtyarenko K. and Contrino S. (2004) COMe: the ontology of bioinorganic proteins. BMC Structural Biology 2004, 4:3 http://www.biomedcentral.com/1472-6807/4/3/


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