title: ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
abstract: BACKGROUND
  Many entries in the protein data bank (PDB) are annotated to show their component protein domains according to the Pfam classification, as well as their biological function through the enzyme commission (EC) numbering scheme. However, despite the fact that the biological activity of many proteins often arises from specific domain-domain and domain-ligand interactions, current on-line resources rarely provide a direct mapping from structure to function at the domain level. Since the PDB now contains many tens of thousands of protein chains, and since protein sequence databases can dwarf such numbers by orders of magnitude, there is a pressing need to develop automatic structure-function annotation tools which can operate at the domain level.
  
  
  RESULTS
  This article presents ECDomainMiner, a novel content-based filtering approach to automatically infer associations between EC numbers and Pfam domains. ECDomainMiner finds a total of 20,728 non-redundant EC-Pfam associations with a F-measure of 0.95 with respect to a "Gold Standard" test set extracted from InterPro. Compared to the 1515 manually curated EC-Pfam associations in InterPro, ECDomainMiner infers a 13-fold increase in the number of EC-Pfam associations.
  
  
  CONCLUSIONS
  These EC-Pfam associations could be used to annotate some 58,722 protein chains in the PDB which currently lack any EC annotation. The ECDomainMiner database is publicly available at http://ecdm.loria.fr/ .
authors.affiliation: Université de Lorraine, LORIA, UMR, Vandœuvre-lès-Nancy, 7503, 54506, France.|Inria Nancy Grand-Es, Villers-lès-Nancy, 54600, France.
authors.forename: Seyed Ziaeddin
authors.initials: SZ
authors.lastname: Alborzi
authors.affiliation: Université de Lorraine, LORIA, UMR, Vandœuvre-lès-Nancy, 7503, 54506, France.|CNRS, LORIA, UMR, Vandœuvre-lès-Nancy, 7503, 54506, France.
authors.forename: Marie-Dominique
authors.identifier: http://orcid.org/0000-0002-0399-8713
authors.initials: MD
authors.lastname: Devignes
authors.affiliation: Inria Nancy Grand-Es, Villers-lès-Nancy, 54600, France. dave.ritchie@inria.fr.
authors.forename: David W
authors.initials: DW
authors.lastname: Ritchie
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D004798:Enzymes; D011506:Proteins
keywords: Content-based filtering; Enzyme commission number; Pfam domain; Protein domain; Protein function