SABIO-RK: Integration and Curation of Reaction Kinetics Data

Abstract

Abstract. Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about biochemical reactions and their kinetic properties. The data are manually extracted from literature and verified by curators, concerning standards, formats and controlled vocabularies. This process is supported by tools in a semi-automatic manner. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases enable the user to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file, allowing users to employ the information as the basis for their simulation models.

On the use of PIPSA to Guide Target‐Selective Drug Design

“…All related DHFR sequences for which kinetic data are available either in BRENDA [14] or SABIO-RK [15] were then retrieved from SwissProt [16] and aligned to the template using CLUSTALW [17] and T-COFFEE. [18] Based on the alignment, homology models were generated automatically with Modeller.…”

Computational optimization and biological evolution

“…Kinetic parameter values, which can be used as constraints for objective functions, can be found in quantitative biochemistry databases [8], whereas enzyme kinetic data can be obtained from BRENDA [9] or SABIO-RK [10].…”

Designing and encoding models for synthetic biology

“…In addition to offering multiple analysis methods, WEBCELL also allows import and modification of models from Biomodels database and JWS online. An interesting approach is adopted by SYCAMORE (Weidemann et al 2008), which merges a database of quantitative enzyme kinetics-SABIO-RK ( Wittig et al 2006)-with the ability to create models via a web front end. These can subsequently be downloaded in the SBML format.…”