News (July 2016)

Increase in the data content of BRENDA in the last years

 
July 2007
July 2008
July 2009
July 2010
July 2011
July 2012
July 2013
July 2014
July 2015
July 2016
Increase from 2007 to 2016
KM VALUES * ENZYMES * ORGANISMS*
79,431
89,012
100,155
110,297
113,332
121,298
126,725
133,580
136,392
141,365
61934 (78%)
KI VALUES*
15,736
19,018
23,700
27,966
31,645
33,819
35,400
36,373
37,491
39,042
23,306 (148%)
pI VALUES*
2,060
2,477
3,067
3,562
3,916
4,251
4,326
4,644
4,825
5,018
2,958 (144%)
IC50 VALUES*
0
842
16,105
25,102
32,658
39,056
42,341
44,909
47,527
50,580
50,580
2D STRUCTURES OF ENZYME LIGANDS
38,488
51,606
63,093
74,979
85,507
99,733
109,264
112,456
113,775
122,631
84,143 (219%)
ENZYME LIGANDS*
764,282
849,197
942,772
1,033,523
1,094,165
1,152,437
1,258,645
1,435,021
1,502,677
1,556,053
791,781 (104%)
ENZYME INHIBITORS*
112,470
127,146
147,962
169,273
189,610
203,727
213,686
218,735
225,795
233,616
121,146 (108%)
ENZYME ACTIVATING COMPOUNDS*
18,466
20,306
23,167
26,508
28,238
29,068
30,404
30,426
31,067
31,538
13,072 (171%)
NATURAL SUBSTRATES OF ENZYMATIC REACTIONS*
51,123
58,296
64,507
71,628
76,255
81,099
97,444
102,754
109,650
115,919
64,796 (127%)
ENGINEERING/MUTATIONS*
23,234
30,437
39,905
48,366
54,821
59,841
64,438
72,591
80,942
82,500
59,266 (255%)
SEQUENCES
283,138
629,980
843,200
1,164,575
1,704,881
2,379,665
4,033,680
6,801,159
12,263,175
7,230,588
6,947,450 (2454%)
SOURCE TISSUE*
44,110
53,547
64,291
74,817
83,090
87,632
90,627
96,298
100,958
101,897
57,787 (131%)
LOCALIZATION*
19,011
21,857
24,757
27,403
29,229
30,894
32,508
36,194
37,944
38,805
19,794 (104%)
REFERENCE CITATIONS
108,887
113,626
130,530
145,130
157,280
165,237
184,540
193,516
201,940
208,234
99,347 (91%)
LITERATURE REFERENCES
68,366
78,598
91,441
102,347
112,389
118,646
122,736
128,108
132,579
136,877
68,511 (100%)
EC CLASSES
4,762
4,824
4,933
5,116
5,372
5,725
6,137
6,549
6,763
6,958
2,196 (46%)
ENZYME SYNONYMS
53,389
67,566
83,459
99,776
112,398
121,001
155,386
159,874
170,794
178,071
124,682 (234%)
* = The numbers denote the enzyme-organism-(protein-)commentary-reference-specific occurrences. For kinetic values (Km, Ki, kcat) and ligand-specific fields (Inhibitors, Activating Compounds, Ligands) the corresponding enzyme ligand is also taken into account.
For example, when the identical pI (isoelectric point) was measured for different enzymes or the identical enzyme from different organisms the information is included for each EC number and organism-specific enzyme isoform, respectively.

New Features & Functionalities in January 2017

  • TaxonomyTree extended by BRENDA strains
  • Revision of the organism-specific pathways
  • Revision of the ligand summary pages (according to the result pages in release 2016.2)
  • new tutorials (video and pdf)
  • BKMReact extended by SabioRK reactions
  • Links to DoGSiteScorer (software to detect potential binding pockets) and ProToss (fully automated hydrogen prediction tool for protein-ligand complexes) from the result pages of the 3D Structure Search

New Features & Functionalities in July 2016

  • New BRENDA pathway maps are online. Pathways can be selected for an indivdual organism or for a taxonomic group.
  • The BRENDA start page is modified in order to present a new and modern easy-to-use interface.
  • Revision of the result pages for a better user experience:
    • Further acceleration of the display..
    • Sortable columns in all data fields.
    • Hide and show data fields.
    • Improved print functions.

New Features & Functionalities in July 2015

  • The BRENDA pathway maps are online. 280 pathways can be displayed. They show ~2000 enzyme-catalyzed reactions. All metabolites and cofactors are linked to the BRENDA data.
  • The new MeSH ontology based on www.nlm.nih.gob/mesh now includes diesease terms and enzyme-disease relations
  • Links to the Biochemical Reaction Kinetics Database SABIO RK in the result pages
  • Acceleration of the result page display

New Features & Functionalities in January 2015

  • The BRENDA Web interface is completely modified and presents a new and modern easy-to-use interface.
  • Word Maps are introduced for 3400 EC classes. The more frequently a word is specifically associated with an enzyme in a literature text, the more prominent it will be presented in the word map. Colors and links are used to provide information of the displayed term.
  • The Enzyme Detector (ED) has been upgraded and equipped with a new algorithm. More data are included in the calculation. These improvements lead to better predictions with a better reliability.
  • The BKM (Biochemical Reactions Aligned) website has been improved. It contains ~22,000 unique enzyme-catalyzed reactions on natural substrates i.e. twice as much as any of the three integrated database (BRENDA, KEGG, MetaCyc).

New Features & Functionalities in July 2014

  • The human anatomy atlas CAVEman an ontology for body parts, organs and tissues was included. The terms were linked to the BRENDA tissue terms.
  • BRENDA-Professional provides INChI strings for Ligand structures (http://www.genexplain.com).

New Features & Functionalities in January 2014

  • Strain denominations were added to microorganisms. Enzyme information can be searched and displayed for single strains.

New Features & Functionalities since 2009

In 2009 the content of BRENDA has been substantially increased (see also table above). In addition, many new features & functionalities have been added to the web interface.

The most important recent developments are:

  • ca. 30,000 new literature references since 2009
    The total amount of manually evaluated literature references comprises now more than 120,000 enzyme-specific references.

  • DRENDA (Disease Related ENzyme information DAtabase) - Improvement of the disease-centered textmining approach
    Automated detection of many enzyme-disease relationships by an enhanced disease mining approach which increases the number of literature references in this field by more than tenfold (now more than 400,000 references automatically annotated):
    Search Disease/Diagnostics

  • KENDA (Kinetic ENzyme DAta)
    KENDA is a new supplement to the BRENDA database providing an additional overview on functional kinetic data of enzymes.This additional resource is based on a text-mining resource extracting kinetic values and expressions (KM, Ki, kcat, Vmax etc.)
    Search KENDA

  • BKM-react
    BKM-react is an integrated and non-redundant biochemical reaction database containing known enzyme-catalyzed and spontaneous reactions. Biochemical reactions collected from BRENDA (BRaunschweig ENzyme DAtabase), KEGG, and MetaCyc were matched and integrated by aligning substrates and products.
    Search BKM-react

  • New ligand summary view
    This new site enhances the search for the more than 105,000 enzyme ligands (small molecules) contained in BRENDA. It constitutes a ligand-centric view to the BRENDA data as a complement to the enzyme-centric view of the enzyme summary page (see e.g. EC 1.2.3.4):
    Example for a Ligand Summary View

  • Distribution of Functional Enzyme Parameters
    This new site displays the frequency distribution (histogram) of a functional enzyme parameter such as the number of enzymes for different Km value ranges. It also allows to focus on one of the six EC main classes or the three main taxonomic groups (Archaea, Bacteria, Eukaryota):
    Histograms of Functional Enzyme ParametersFunctional Enzyme Parameters

  • Enhanced view of enzyme 3D structure
    The search site for 3D structure/PDB link now offers the possibility to display the protein sequence motifs in the 3D structure of an enzyme.
    It offers e.g. access to 360,987 active sites, 624,866 metal ion-binding sites and 182,223 nucleotide phosphate-binding regions.
    Example for the enhanced 3D enzyme structure view (marked in yellow)

  • New protein-specific display option for enzymes
    The enzyme summary page was expanded by a protein-specific enzyme search/display option which allows to focus on a single enzyme isoform (protein variant) of the organism of interest. The specification is done via the UniProt Acc.:
    Search for UniProt Accessions

  • Inclusion of MetaCyc pathways
    The Search Pathway form was expanded to also include metabolic pathways MetaCyc (in addition to the KEGG pathways):
    Search Pathway

  • New SBML output option for enzyme-kinetic parameters
    The new site allows the construction of organism-specific metabolic models from BRENDA data using the SBML (Systems Biology Markup Language) format:
    SBML Output Site SBML Logo

  • Improvement of the disease-centered textmining approach
    Automated detection of many enzyme-disease relationships by an enhanced disease mining approach which increases the number of literature references in this field by more than tenfold (now more than 400,000 references automatically annotated):
    Search Disease/Diagnostics