DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
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The University of Minnesota Biocatalysis / Biodegradation Database"  info
 

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
http://eawag-bbd.ethz.ch/

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.
http://biocyc.org/open-compounds.shtml

BRaunschweig ENzyme DAtabase"  info
 

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.
The development of an enzyme data information system was started in 1987 at the German National Research Centre for Biotechnology in Braunschweig (GBF) and is now continued at the University of Cologne, Institute of Biochemistry.
http://www.brenda-enzymes.info/

Catalytic Site Atlas (CSA)
 

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
http://www.ebi.ac.uk/thornton-srv/databases/CSA/

Dehydrogenase Enzyme Stereospecificities Database"  info
 

The Dehydrogenase Stereospecificity Database(DSD) provides a compilation of enzyme stereochemical data.
http://www.darrenflower.info/DSD/dehydrog.htm

Enzymes and Metabolic Pathways database (EMP)
 

Enzymes and Metabolic Pathways database, EMP, is a unique and most comprehensive electronic source of biochemical data. It covers all aspects of enzymology and metabolism and represents the whole factual content of original journal publications.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+EMP

Enzyme (EMBL)
 

The ENZYME data bank contains the following data for each type of characterized enzyme for which an EC number has been provided: EC number, Recommended name, Alternative names, Catalytic activity, Cofactors, Pointers to the SWISS-PROT entrie(s) that correspond to the enzyme, Pointers to disease(s) associated with a deficiency of the enzyme.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+ENZYME

Enzyme Nomenclature Database
 

The ENZYME database is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB), and it contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided:

  • EC number
  • Recommended name
  • Alternative names (if any)
  • Catalytic activity
  • Cofactors (if any)
  • Pointers to the Swiss-Prot protein sequence entrie(s) that correspond to the enzyme (if any)
  • Pointers to human disease(s) associated with a deficiency of the enzyme (if any)
    http://us.expasy.org/enzyme/

  • Enzyme Nomenclature Database
     

    Enzyme Nomenclature. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
    http://www.chem.qmw.ac.uk/iubmb/enzyme/

    ESTerases and alpha / beta Hydrolase Enzymes and Relatives
     

    This server is dedicated to the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.
    http://bioweb.ensam.inra.fr/ESTHER/general?what=index

    Integrated Relational Enzyme Database
     

    The Integrated relational Enzyme database (IntEnz) will contain enzyme data approved by the Nomenclature Committee. The goal is to create a single relational enzyme database.
    http://www.ebi.ac.uk/intenz/index.html

    LIGAND, Database of Chemical Compounds and Reactions in Biological Pathways
     

    LIGAND, Database of Chemical Compounds and Reactions in Biological Pathways, is designed to provide the linkage between chemical and biological aspects of life in the light of enzymatic reactions. The database consists of four sections: COMPOUND, GLYCAN, REACTION, and ENZYME The COMPOUND section is a collection of metabolic and other compounds including substrates, products, inhibitors of metabolic pathways as well as drugs and xenobiotic chemicals. Each of the chemical substances that appear in the REACTION and ENZYME sections and KEGG/PATHWAY database is identified by an accession number and stored in this section. Each entry of COMPOUND contains information of naming, chemical formula, structural formula in a separate GIF file and a MOL file, metabolic and other pathways, related enzymes, related protein structures, prosthetic groups and CAS (Chemical Abstracts Service) registry number.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+LCOMPOUND

    Lipase Engineering Database"  info
     

    The Lipase Engineering Database (LED) integrates information on sequence, structure, and function of lipases, esterases, and related proteins.
    http://www.led.uni-stuttgart.de/

    Mechanism, Annotation and Classification in Enzymes
     

    MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a unique database of enzyme reaction mechanisms, focusing on well characterised enzymes with PDB entries and relatively well understood mechanisms. All mechanisms have been taken from the primary literature and curated by a trained chemist and biochemist. MACiE is a collaborative project between the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.
    http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

    Multiorganism Database of Metabolic Pathways and Enzymes"  info
     

    MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways from more than 300 different organisms.
    http://metacyc.org/

    A Protein Phosphatase Information Resource"  info
     

    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.
    http://bioinf.man.ac.uk/phosphabase/index.html

    Pyridoxal 5'-Phosphate Dependent Enzymes Mutants Database"  info
     

    The PLPMDB database provides access to relevant mutant information on Pyridoxal-5'-phosphate dependent enzymes.
    http://www.studiofmp.com/plpmdb/index.htm

    Predicted and Consensus Interaction Sites in Enzymes"  info
     

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.
    http://precise.bu.edu/precisedb/

    Predicted and Consensus Interaction Sites in Enzymes"  info
     

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.
    http://precise.bu.edu/

    Structure-Function Linkage Database"  info
     

  • SFLD is a database that links evolutionarily related sequences and structures from mechanistically diverse superfamilies of enzymes to their chemical reactions.
  • Correlates conserved active site residues with specific partial reactions that all members of a superfamily perform.
    http://sfld.rbvi.ucsf.edu/

  • Thermodynamics of Enzyme-Catalyzed Reactions
     

    Database about the thermodynamics of encyme-catalyzed reactions, made by Robert N. Goldberg, Yadu B. Tewari and T.N.Bhat, Biotechnology Division, National Institute of Standards and Technology Gaithersburg,
    http://xpdb.nist.gov/enzyme_thermodynamics/

    UENZYME
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UENZYME

    UIMAGEMAP
     

    UIMAGEMAP contains all the graphic-based pathways in UMBBD.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UIMAGEMAP

    UPATHWAY"  info
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UPATHWAY

    UREACTION
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UREACTION