Molecular Biology Databases on the Net
This is not intended to be complete. Go to ExPASy
Molecular Biology Server for the most complete list of links that I know
of. In ExPASy, click on 'Links to many other molecular biology databases'
for a huge list of Databases.
In the following you find some links to databases I use frequently for
Modelling Pathways:
This database includes Metabolic Pathways as nice maps. Links on the maps
allow direct access to information about metabolites and enzymes, including
structural forms, chemical composition, and much more. My favorite features
of KEGG:
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Pathways can be shown organism specific.
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Pathway calculation: given two substrates, let KEGG search for possible
pathways between these substrates.
The complete set of tools from KEGG are:
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PATHWAY Maps: Search enzymes, compounds, or genes in the PATHWAY
database
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GENOME Maps:
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Search gene positions, homologous gene clusters in the GENOME map
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Compare two genome maps for exhaustive search of homologous gene clusters
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Coloring Tools: Color genes in the PATHWAY or GENOME map
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Prediction Tools:
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Reconstruct pathways by BLAST search of KEGG pathway diagrams
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Reconstruct pathways by FASTA search of KEGG ortholog group tables
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Generate possible reaction pathways between two compounds
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Sequence Similarity
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FASTA or BLAST search of similar amino acid sequences in the GENES database
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FASTA or BLAST search of similar nucleotide sequen
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ces in the whole GENOME database
Enzymatic Reaction Properties:
To find information about the role of an enzyme for a specific reaction,
the best strategy seems a search in
ExPASy
ENZYME by EC-number (can be found e.g. from the KEGG
pathway map). As a result, enzyme description is given, and links to:
BRENDA:
Click to get enzyme structure, corresponding reactions, inhibitors,
activators, Km values, literature, and much more
WIT:
Pathway connections and link to 'EMP-Records' which provides lots of
literature to the specific enzyme, including data from this literature
(kinetic type, Km values, turnover rates etc.).
EcoCyc (Encyclopedia of
E. coli Genes and Metabolism)
This ecoli specific database includes pathway maps in nice form, similar
to the KEGG database. You need to register (free for non-profit organizations).
EMBL - European Bioinformatics Institute
(EBI)
EMBL is a centre for research and services in bioinformatics. The Institute
manages databases of biological data including nucleic acid, protein sequences
and macromolecular structures. Provides also access to many databases on
the net.
URL:
<http://www.fz-juelich.de/ibt/ferm/hurlebaus/databaselinks.html>
