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. 2017 Jan 4;45(D1):D380-D388.
doi: 10.1093/nar/gkw952. Epub 2016 Oct 19.

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek  1 , Ida Schomburg  1 , Antje Chang  1 , Lisa Jeske  1 , Marcus Ulbrich  1 , Jana Tillack  1 , Dietmar Schomburg  2
Affiliations

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek et al. Nucleic Acids Res. .

Abstract

The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External data and links complete the data with sequences and 3D structures. A total of 206 000 enzyme ligands provide functional and structural data. BRENDA offers a complex query tool engine allowing the users an efficient access to the data via different search methods and explorers. The new design of the BRENDA entry page and the enzyme summary pages improves the user access and the performance. New interactive and intuitive BRENDA pathway maps give an overview on biochemical processes and facilitate the visualization of enzyme, ligand and organism information in the biochemical context. SCOPe and CATH, databases for protein structure classification, are included. New online and video tutorials provide online training for the users. BRENDA is freely available for academic users.

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Figures

Figure 1.
Figure 1.
Inhibitor table of acetylglutamate kinase: rows with redundant entries are merged to a single line. The inhibitor arginine is listed with different organisms and commentaries in 10 lines of information. The user can click at the (+)-icon to show the specific data of an inhibitor or click at the (−)-icon to hide it.
Figure 2.
Figure 2.
Several print options on the enzyme summary page: (A) It is possible to print all tables of the page or only those, which are currently visible. (B) The red bordered function can be used to print a table separately.
Figure 3.
Figure 3.
Overview map with pathway icons colored differently with respect to their metabolic roles. The pathways are categorized as central and energy metabolism (red), lipid metabolism (orange), amino acid metabolism (green), nucleotide and cofactor metabolism (blue), carbohydrate metabolism (yellow), fermentation and other catabolism (dark gray) and xenobiotics and secondary metabolism (light gray). This color scheme will be available in Release 2017.1.
Figure 4.
Figure 4.
Taxonomic overview map showing the metabolic repertoire for Zymomonas mobilis including all taxonomically related organisms up to the genus bacterium. The taxonomic range is indicated by a coloring scheme. The further up in the taxonomic range the lighter the color becomes.
Figure 5.
Figure 5.
Pathway map of phenylalanine metabolism with metabolites (blue rectangles), enzymes (red ellipses) and hidden co-metabolites. Co-metabolites can be switched on or off using the ‘on/off’-button in the right upper corner.
Figure 6.
Figure 6.
Distribution of unique reactions between BRENDA, KEGG and MetaCyc in BKM-react.
See this image and copyright information in PMC

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