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Web Site BRENDA Everything You Always Wanted To Know about Enzymes.

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Web Sites
BRENDA: Everything You Always
Wanted To Know about Enzymes
Dont worry—you can add BRENDA to
your bookmarks without blushing. Shes
not a shady lady, but a perfectly respectable scientific tool: the BRENDA database (BRaunschweig ENzyme DAtabase) was founded in 1987 by Dietmar
Schomburg and has since been transferred to the Universit,t K.ln.[1] BRENDA is a comprehensive collection of
enzyme data as found in the primary
literature—a sort of digital encyclopedia
of enzymes. Because of the large scope
of this group of proteins and the torrent
of data from biomedical research, this is
a Herculean task. Accordingly, the
amount of data available on the site is
impressive.
At present, BRENDA contains data
on the functional and molecular properties of more than 40 000 individual
enzymes from almost 5000 different
organisms and covering more than
4000 enzyme numbers (IUBMB enzyme
nomenclature). Here we find the reaction catalyzed by each enzyme, but also
parameters such as optimal pH value
and temperature, chemical and thermal
stability, and details about purification
and crystallization. These data are compiled from more than 50 000 references.
Moreover, a large number of enzyme –
ligand interactions are recorded
(438 000 entries on substrates, inhibitors,
activators, and cofactors). The ligands
are saved with their name, but also as
SMILES and molfiles, that is, in forms
containing structural information. This
allows not only the 2D visualization of
structural formulae, but also substructure-based searching, through which,
starting from a molecular substructure,
one can find ligands containing these
structural components. Last but not
5666
Figure 1. BRENDA: A resource for enzyme data and metabolic information.
least, disease-related information is included for almost 1000 enzymes. At
present the primary literature is still
sifted manually, but automated data
extraction is being developed.
BRENDA is a relational database,
which means that all data are organized
in tables that are linked to one another.
All data fields can be accessed directly
from the main page (see Figure 1). The
individual enzyme entries are directly
linked to the respective sequence entries
in the sequence database Swiss-Prot/
TrEMBL and the 3D structures in the
Protein Data Bank (PDB), and the
references are linked to the PubMed
entries. Enzymes can be searched for
most easily by EC number, enzyme
name, or organism, but combined
searches (“advanced search”) are also
possible.
data collection on a single website. On
the one hand a unified representation is
in the interests of the user, but on the
other hand the single-site approach fails
to make use of some advantages that the
internet offers today. I would prefer a
more direct link to other databases that
are specialized in particular groups
of enzymes, such as kinases or hydrolases—links that can be used directly
from an enzyme entry and not only from
a general list of “useful links” provided
elsewhere. Nonetheless, BRENDA is a
good place to start when you need
information about a particular enzyme.
BRENDA is accessible free of charge
for academic purposes; commercial
users need a license, which is available
from www.science-factory.com
Christoph Weise
Institut fr Chemie-Biochemie
der Freien Universitt Berlin (Germany)
Suggest a web site or submit a review:
angewandte@wiley-vch.de
On the down side, there are still
many respects in which the site could be
made more user-friendly. In particular, a
help function is needed to facilitate
navigation of the text and numerical
fields for advanced searches. Another
weak point is the lack of a graphical
representation of the metabolic pathways in which the enzymes are involved.
It is even debatable whether it still
makes sense to have a comprehensive
- 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
[1] I. Schomburg, A. Chan, O. Hofmann, C.
Ebeling, F. Ehrentreich, D. Schomburg,
Trends Biochem Sci. 2002, 27, 54 – 56.
For more information visit
http://www.brenda.uni-koeln.de/
or contact
D.Schomburg@uni-koeln.de
Angew. Chem. Int. Ed. 2003, 42, 5666
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