News (July 2012)

Increase in the Data Content of BRENDA in the Last Years

	July 2007	July 2008	July 2009	July 2010	July 2011	July 2012	Increase from 2007 to 2012
KM VALUES * ENZYMES * ORGANISMS*	79,431	89,012	100,155	110,297	113,332	121,298	41,867 (53%)
KI VALUES*	15,736	19,018	23,700	27,966	31645	33,819	18,083 (117%)
pI VALUES*	2,060	2,477	3,067	3,562	3,916	4,251	2,191 (106%)
IC50 VALUES*	0	842	16,105	25,102	32,658	39,056	39,056
2D STRUCTURES OF ENZYME LIGANDS	38,488	51,606	63,093	74,979	85,507	99,733	61,245 (159%)
ENZYME LIGANDS*	764,282	849,197	942,772	1,033,523	1,094,165	1,152,437	388,155 (51%)
ENZYME INHIBITORS*	112,470	127,146	147,962	169,273	189,610	203,727	91,257 (81%)
ENZYME ACTIVATING COMPOUNDS*	18,466	20,306	23,167	26,508	28,238	29,068	10,602 (57%)
NATURAL SUBSTRATES OF ENZYMATIC REACTIONS*	51,123	58,296	64,507	71,628	76,255	81,099	29,976 (59%)
ENGINEERING/MUTATIONS*	23,234	30,437	39,905	48,366	54,821	59,841	36.607 (158%)
SEQUENCES	283,138	629,980	843,200	1,164,575	1,704,881	2,379,665	2,096,527 (740%)
SOURCE TISSUE*	44,110	53,547	64,291	74,817	83,090	87,632	43,522 (99%)
LOCALIZATION*	19,011	21,857	24,757	27,403	29,229	30,894	11,893 (63%)
REFERENCE CITATIONS	108,887	113,626	130,530	145,130	157,280	165,237	56,350 (52%)
LITERATURE REFERENCES	68,366	78,598	91,441	102,347	112,389	118,646	50,280 (74%)
EC CLASSES	4,762	4,824	4,933	5,116	5,372	5,725	963 (20%)
ENZYME SYNONYMS	53,389	67,566	83,459	99,776	112,398	121,001	67,612 (126%)

* 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 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 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

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