SABIO-RK

[…] rning algorithms can give better predictions with more correctly labeled “big data”. Hence, a database of DNA sequences and the corresponding enzyme substrate and enzyme activity (such as BRENDA and SABIO-RK ) should be included in machine learning workflow to predict enzyme-substrate pairs with high likelihood for interaction.When natural enzymes fail to perform the predicted reaction steps, pro […]

[…] ms for organisms, tissues, kinetic parameters or kinetic rate laws. A partial screenshot of the Visual search containing the diagrams for organisms and tissues is shown in Figure .Search results of a SABIO-RK query can be selected for export by collecting database entries in an export cart. Data can be exported in standard exchange formats including SBML (), BioPAX (), SBPAX (), MatLab (http://www […]

[…] perform enrichment or overrepresentation analysis, eg, of patient molecular data. BioModels and JWS are repositories for mathematical models of biological systems, while databases such as Brenda and SABIO-RK provide additional information on reaction kinetics and kinetic parameters. Detailed information on molecular species and drugs can be found in databases such as ChEMBL. An overview of the fr […]

[…] and glycogen and G6P content, as measured at the end of the simulation. The kinetic behavior of the pentose–phosphate pathway was described by the kinetic laws published in a previous report and the SABIO-RK database. These kinetic data were implemented into a model formed using systems biology markup language (File S2). Simulations based on this model were performed using MATLAB 2012b. The gluta […]

[…] of metabolism from a number of organisms [,]. Enzymes and their kinetic properties are found in various generic and model organism-specific databases which are curated and are included in Uniprot [], SABIO-RK [].A combination of tools is required to model a biological system mathematically []. The process begins by mapping the information for each biochemical reaction and its parameters from its s […]

[…] ived from pathway resources (Figure A(b)). The pathway information from data resources such as the Kyoto Encyclopedia of Genes and Genomics, BioCarta/Nature Pathway Interaction Database, MetaCyc, and SABIO-RK are automatically converted into standard-compliant computational models. Multiple biological processes, described in 2,616 organisms, were converted into computational models encoded in the […]