Martin DAVY1, Patrick AMAR1,2
1 Synthetic & Systems Biology group, Sys2diag UMR 9005 CNRS, ALCEN
2 Bioinfo group, LISN, Univ. Paris Saclay, UMR 9015 CNRS
|Windows Version (September 16, 2020)|
|Linux (x86_64) Version (September 16, 2020)|
|Mac OS X (High Sierra) Version (September 16, 2020)|
BrendaXplorer is a tool to extract sub-networks from a reaction database, such as BRENDA ( https://www.brenda-enzymes.org). It is used along with Silicell Maker to automatically build the initial biochemical network used to find enzymatic logic gates.
The Master memoir of Martin DAVY can be viewed here (1.9 Mb PDF).
When launched, BrendaXplorer displays a dialog box where all main parameters can be input. The reactions and inhibitions data banks are CSV files obtained from the text extraction of the BRENDA database by a preprocessor filter. The reaction list is a CSV file output by BrendaXplorer that lists all the reactions catalysed by the enzymes used in the output network built.
The generated network obtained from the parameters given in the dialog box is shown below (input metabolites: starch output metabolites: H2O2, with at most 2 reactions between input ant output and using enzymes working with a pH between 7 and 8).
|Website designed & maintained by Patrick Amar (patrick DOT amar AT sys2diag DOT cnrs DOT fr)|