BRENDA enzymes database

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enzymes database

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BRENDA:

BRENDA Largest enzyme function Relational database created in 1987 at GBF and maintained by University of Cologne Till 2003,it provided information of 83,000 different enzymes along with 4,200 EC numbers about 9800 organisms. data is freely accessible as a text file from 2007 Enzymes from 105000 organisms are characterized www. brenda -enzymes.org

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Organism coverage on BRENDA data Fig.#1

INFORMATION:

INFORMATION Organism-specific information on functional and molecular properties Reaction and specificity Enzyme structure Stability Application and engineering Ligands Literature references Links to other database

QUICK SEARCH MODE:

QUICK SEARCH MODE Write amylase name, EC number etc.

FULL TEXT SEARCH:

FULL TEXT SEARCH

ADVANCE SEARCH MODE:

ADVANCE SEARCH MODE

Substructure search:

Substructure search

taxtree:

taxtree organisms integrated into Tax Tree Overview of species linked to the NCBI taxonomy database Few are cannot linked as they are not in NCBI taxonomy tree.

taxtree:

taxtree

EC EXPLOROR:

EC EXPLOROR Enzyme Commission number numerical classification scheme for enzymes based on the chemical reactions they catalyze.

Sequence search:

Sequence search

GENOME EXPLORER:

GENOME EXPLORER Genome visualization tool Allows alignment of genome at enzyme coding gene

ONTOLOGY EXPROLER:

ONTOLOGY EXPROLER

ONTOLOGY FOR ENZYM SOURCE:

ONTOLOGY FOR ENZYM SOURCE BRENDA tissue ontology number Multi-cellular organism source Whole body Single tissue Normal tissue Cancerous tissue Tissue tree E.g. animal body divided in 18 sub-trees Skeletal Hematopoietic Visceral cancer cell type or cell line

FUNCTIONAL ENZYME PARAMETERS:

FUNCTIONAL ENZYME PARAMETERS Data is shown in bar diagrams Distribution of k m value, k cat value, PH optimum, temperature optimum etc.

SMBL OUTPUT FORM:

SMBL OUTPUT FORM System biology markup language- an XML Based format For the transfer of data to tolls and programs Execution of MySQL statement is possible Query results are extracted, converted to CSV format, then to SBML CODE Organism specific information on the biochemical properties and kinetic parameters

SOAP:

SOAP Simple object access protocol SOAP based web service API Covers 50 different data fields Provides access via more than 150 different methods

LOCALIZATION:

LOCALIZATION Part of cell where enzyme is located Vocabulary for localization terms GO-numbers amiGO tree view

LIGAND SUMMARY PAGE:

LIGAND SUMMARY PAGE Natural or in vitro Substrate, Products, Inhibitors, Activation compounds, Cofactors, Bound metals etc. Approx. 500000 enzyme- ligand relationships are stored 46000 ligands 2D images are provided

BRENDA-LIGAND THESAURUS:

BRENDA-LIGAND THESAURUS Enzyme- ligand related information Provides search for all synonyms Systematic name, Chemical compound, trivial name, abbreviation

BRENDA-LIGAND SUBSTRUCTURE SEARCH:

BRENDA-LIGAND SUBSTRUCTURE SEARCH Sub-graph matching searches Two search steps Prefilter -fast fingerprint scan Sub graph matching Can be edited or uploaded by structure sketch tool

3D STRUCTURE OF ENZYME:

3D STRUCTURE OF ENZYME Visualization of 3D structure 3D structure/PDB query followed by the selectin of 3D View Visualization tool Jmol Features displayed are:

Visualization:

Visualization

METABOLISM:

METABOLISM Calculation and simulation of metabolic pathways Information of substrate product chains Kinetic data Navigation operations can be made Linked to KEGG and Metacyc databases

ENZYME AND DISEASE INFORAMTION:

ENZYME AND DISEASE INFORAMTION 786 enzymes information associated with human diseases Linked to PUBMED and OMIM Based on text mining procedure AMENDA FRENDA www. brenda -enzymes.org

PowerPoint Presentation:

Thank you

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