SABIO-Reaction Kinetics Database

Sabio -RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics ) is a web- accessible database which stores comprehensive information about biochemical reactions and their kinetic properties.

Unlike other databases, which either enzyme database ( BRENDA ) or protein database ( UniProt ) or model database ( BioModels, JWS Online) have been created, Sabio -RK represents a reaction - oriented database with quantitative information on the reaction dynamics.

The dynamics of biochemical reactions is of central importance in biology and medicine for the understanding of cellular processes and in the development of drugs. The experimentally obtained data for the quantitative description of reaction dynamics and enzyme kinetics are manually extracted from the literature and stored in a standardized form in Sabio -RK. The contents of the database comprises kinetic parameters with respect to biochemical reactions, and their biological sources. In addition, kinetic rates of speed of enzymes and the corresponding equations and the corresponding experimental conditions are stored. All data are manually curated biological experts and commented, supported by automated consistency checks. On Sabio -RK can be accessed via web-based user interface or automatically via web services. Both interfaces support the export of the data together with corresponding annotations in SBML ( Systems Biology Markup Language ), for example, for import into modeling tools. Sabio -RK is maintained at the Heidelberg Institute for Theoretical Studies (HITS ) and further developed.

Currently 42846 individual kinetic records are stored in Sabio -RK, which come from over 3966 publications (as of December 2012). From these records, about 43 % are attributable to the Michaelis- Menten type (more than 33700 ' Km values ​​'), 30880 kinetic parameters correspond to constants (Vmax, kcat, rate constants ). Kinetic data are available for 737 organisms, 5605 reactions and almost 1255 different enzymes. Annotations are carried out at a number of other databases, including KEGG, ChEBI, PubChem, UniProt, NCBI and PubMed.

Access to Sabio -RK

For academic and non-commercial users, the use of Sabio -RK is free. Commercial users need a license. The stored data can be accessed in several ways:

  • Web - based (browser): the database can now be searched using various criteria according to the kinetic data. These criteria include, inter alia, the search for substrates, products, coenzymes, inhibitors, enzyme names, EC numbers, tissues, organisms, publications, kinetic parameter types, cellular localizations or metabolic pathways.
  • In addition, Web Services are made available which the kinetic information on automated request forwarding ( SOAP and RESTful interfaces).
Chemical kinetics Reaction rate constant Enzyme substrate (biology) Tissue (biology) Representational State Transfer Nucleic Acids Research
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