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Sponsor of the Month
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Databases and software
releated to enzymes
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BOCD:
BioCyc Open Chemical Database
"The BioCyc Open Chemical Database (BOCD) is a collection of chemical compound data from the BioCyc databases. Most of the compounds act as substrates in enzyme-catalyzed metabolic reactions, but some compounds serve as enzyme activators, inhibitors, or cofactors. Chemical structures are provided for the majority of compounds. The compounds include extensive lists of synonyms, and have undergone several types of quality control, including validation by a reaction-balance checker applied to the BioCyc databases." |
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BRENDA:
BRaunschweig ENzyme DAtabase
Categories:
Enzyme and Enzyme Nomenclature Databases
BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.
Link: http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D431 |
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Enzyme
Nomenclature
"The complete contents of Enzyme Nomenclature, 1992 (plus
subsequent supplements and other changes) are listed below in enzyme number
order giving just the recommended name. Each entry provides a link to details
of that enzyme. Alternatively if looking for a specific reaction used in
the classification of enzymes the broad outline defined by the first two
numbers are given below. Each of these subclass entries is linked to a location
where the category is subdivided to sub-subclasses. These in turn are linked
to a list of recommended names for each enzyme in the sub-subclass." |
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ENZYME:
Enzyme Nomenclature Database
The ENZYME database is a repository of information related to the nomenclature
of enzymes. In recent years it has became an indispensable resource for
the development of metabolic databases. The current version contains information
on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/
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Link: http://nar.oupjournals.org/cgi/content/full/28/1/304 |
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IntEnz
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz.
Link: http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D434 |
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Kinase
Pathway Database
Protein kinases play a crucial role in the regulation of cellular functions.
Various kinds of information about these molecules are important for understanding
signaling pathways and organism characteristics. We have developed the Kinase
Pathway Database, an integrated database involving major completely sequenced
eukaryotes. It contains the classification of protein kinases and their
functional conservation, ortholog tables among species, protein-protein,
protein-gene, and protein-compound interaction data, domain information,
and structural information. It also provides an automatic pathway graphic
image interface. The protein, gene, and compound interactions are automatically
extracted from abstracts for all genes and proteins by natural-language
processing (NLP).The method of automatic extraction uses phrase patterns
and the GENA protein, gene, and compound name dictionary, which was developed
by our group. With this database, pathways are easily compared among species
using data with more than 47,000 protein interactions and protein kinase
ortholog tables. The database is available for querying and browsing at
http://kinasedb.ontology.ims.u-tokyo.ac.jp/. |
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PhosphaBase:
A Protein Phosphatase Information Resource
PhosphaBase is an ontology-driven database resource containing information
on the protein phosphatase family. It is the first public resource dedicated
to protein phosphatases, which are enzymes that perform dephosphorylation
reactions. In conjunction with the phosphorylation action of protein kinases,
phosphatases are involved in important control and communication mechanisms
in the cell. They have also been implicated in many human diseases, including
diabetes and obesity, cancers, and neurodegenerative conditions. PhosphaBase
aims to centralize the growing base of knowledge in the phosphatase research
domain. The resource is built around a formal, domain-specific DAML+OIL
ontology, and the data are collected from heterogeneous biological sources
using Gene Ontology terms as a means of data extraction. The overall ontology-driven
architecture provides a robust structure with distinct advantages for sustainability
and provides the potential for the development of diagnostic tools, as well
as a data repository.
Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15558746 |
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PKR:
The Protein Kinase Resource
Protein kinases and phosphatases play crucial roles in all the major cellular
processes, such as signal transduction, cell differentiation, cell proliferation
and cell cycle progression. Protein phosphorylation or dephosphorylation
can form the basis of many critical processes, including enzyme activation
or inactivation, protein localization and protein degradation. Given the
importance of protein kinases to cellular development and function, it is
critical that there are effective ways of disseminating information on protein
kinases to the research community. This review describes such a web resource,
'The Protein Kinase Resource' (http://pkr.sdsc.edu/html/index.shtml), which
serves as a repository for cellular and molecular data on protein kinases.
Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15656777 |
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PRECISE:
Predicted and Consensus Interaction Sites in Enzymes
PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database
of interactions between the amino acid residues of an enzyme and its ligands
(substrate and transition state analogs, cofactors, inhibitors and products).
It is available online at http://precise.bu.edu/. In the current version,
all information on interactions is extracted from the enzyme–ligand complexes
in the Protein Data Bank (PDB) by performing the following steps: (i) clustering
homologous enzyme chains such that, in each cluster, the proteins have the
same EC number and all sequences are similar; (ii) selecting a representative
chain for each cluster; (iii) selecting ligand types; (iv) finding non-bonded
interactions and hydrogen bonds; and (v) summing the interactions for all
chains within the cluster. The output of the search is the color-coded sequence
of the representative. The colors indicate the total number of interactions
found at each amino acid position in all chains of the cluster. Clicking
on a residue displays a detailed list of interactions for that residue.
Optional filters allow restricting the output to selected chains in the
cluster, to non-bonded or hydrogen bonding interactions, and to selected
ligand types. The binding site information is essential for understanding
and altering substrate specificity and for the design of enzyme inhibitors.
Link: http://nar.oupjournals.org/cgi/content/full/33/suppl_1/D206 |
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SCOPEC:
a Database of Protein Catalytic Domains
MOTIVATION: Domains are the units of protein structure, function and evolution.
It is therefore essential to utilize knowledge of domains when studying
the evolution of function, or when assigning function to genome sequence
data. For this purpose, we have developed a database of catalytic domains,
SCOPEC, by combining structural domain information from SCOP, full-length
sequence information from Swiss-Prot, and verified functional information
from the Enzyme Classification (EC) database. Two major problems need to
be overcome to create a database of domain-function relationships; (1) for
sequences, EC numbers are typically assigned to whole sequences rather than
the functional unit, and (2) The Protein Data Bank (PDB) structures elucidated
from a larger multi-domain protein will often have EC annotation although
the relevant catalytic domain may lie elsewhere. RESULTS: SCOPEC entries
have high quality enzyme assignments; having passed both computational and
manual checks. SCOPEC currently contains entries for 75% of all EC annotations
in the PDB. Overall, EC number is fairly well conserved within a superfamily,
even when the proteins are distantly related. Initial analysis is encouraging;
suggesting that there is a 50:50 chance of conserved function in distant
homologues first detected by a third iteration PSI-BLAST search. Therefore,
we envisage that a knowledge-based approach to function assignment using
the domain-EC relationships in SCOPEC will gain a marked improvement over
this base line. AVAILABILITY: The SCOPEC database is a valuable resource
in the analysis and prediction of protein structure and function. It can
be obtained or queried at our website http://www.enzome.com
Link:http://bioinformatics.oupjournals.org/cgi/reprint/20/suppl_1/i130 |
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TECRDB:
Thermodynamics of Enzyme-catalyzed Reactions Database
Summary: The Thermodynamics of Enzyme-catalyzed Reactions Database (TECRDB)
is a comprehensive collection of thermodynamic data on enzyme-catalyzed
reactions. The data, which consist of apparent equilibrium constants and
calorimetrically determined molar enthalpies of reaction, are the primary
experimental results obtained from thermodynamic studies of biochemical
reactions. The results from 1000 published papers containing data on 400
different enzyme-catalyzed reactions constitute the essential information
in the database. The information is managed using Oracle and is available
on the Web.
Link: http://bioinformatics.oupjournals.org/cgi/content/abstract/20/16/2874 |
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ERGO
Formally the WIT database,
provides information about the functional role of enzymes. |
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