An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

Abstract

Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al ., Nucleic Acids Res. 2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016; , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res. 2004 , D434-D437) and ChEBI (Hastings, J., et al ., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res. 2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration.

Keywords: Enzymes; integration; proteins; search; services.

Fig. 1

Enzyme Portal architecture.

Fig. 2

Updated Enzyme Portal home page.

Fig. 3

Comparing enzymes through the basket.

Fig. 4

Results for a keyword search with ‘Erlotinib’ showing a result for Receptor protein-tyrosine kinase expanded to show associated proteins.

Fig. 5

Enzyme entry page for EGF Receptor showing tabs on the left hand side.

Fig. 6

Enzyme entry for the EGF receptor in the Enzyme Portal with small molecules listed including inhibitors.

Fig. 7

Browsing Enzyme Portal by pathways and searching for xenobiotics within the pathways page.

Fig. 8

Enzyme results for xenobiotics pathway search.

Fig. 9

Pathway data from the Cytochrome P450 2C9 enzyme entry.

Fig. 10

Sequence search interface linked from the Enzyme Portal home page.