Come: The Ontology of Bioinorganic Proteins

Science Direct Working Paper No S1574-0331(04)70707-9

19 Pages Posted: 6 Jun 2017 Last revised: 13 Jan 2018

See all articles by Kirill Degtyarenko

Kirill Degtyarenko

European Bioinformatics Institute

Sergio Contrino

European Bioinformatics Institute

Date Written: July 2003


COMe (Co-Ordination of Metals) represents the ontology for bioinorganic centres in complex proteins. COMe consists of three types of entities: ‘bioinorganic motif (BIM), ‘molecule’ (MOL), and ‘complex proteins’ (PRX); each entity is assigned a unique identifier. A 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 (1-D) strings and 2-D diagrams. MOL entity represents ‘small molecule’ which, in complex with polypeptide(s), forms a functional protein. The PRX entity refers to the functional protein as well as separate protein domains and subunits. The main groups 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 .

Keywords: Biochemistry > Other, biochem/0307002

Suggested Citation

Degtyarenko, Kirill and Contrino, Sergio, Come: The Ontology of Bioinorganic Proteins (July 2003). Chemistry Preprint Archive Vol. 2003, Issue 7, pp 240-258. Available at SSRN:

Kirill Degtyarenko (Contact Author)

European Bioinformatics Institute ( email )

United Kingdom

Sergio Contrino

European Bioinformatics Institute

United Kingdom

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