Many enzymes are aspecific, or even promiscuous: they can catalyze transformations of more metabolites than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. We have developed a method to model enzyme aspecificity, by predicting whether an input compound is likely to be transformed by a certain enzyme. This system, called MaRIboES (metabolite and reaction inference based on enzyme specificities), has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. MaRIboES employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.
The MaRIboES system is not maintained in SVN here, but the core Matlab code is available in the downloads section. This code is available under a BSD license. The download includes documentation detailing what other components are required and how to obtain them. Please use the latest version (2.1.0 as of January 11, 2011).
- Rogier van Berlo, Marco de Groot and Dick de Ridder (version 1.0).
- Gaspard Lequeux and Dick de Ridder (version 2.0).
- Gaspard Lequeux and Marco de Groot (version 2.1).
Other NBIC software projects
All active NBIC software projects can be accessed from the project index.