GPRuler (metabolic Gene-Protein-Reaction rules automatic reconstruction) is an open-source tool to automate the reconstruction process of gene-protein-reaction (GPR) rules for any living organism, which describe with a Boolean logic relationships between the gene products (e.g., enzyme isoforms or subunits) associated with the catalysis of a given reaction.
By mining text and data from multiple biological databases, GPRuler can reconstruct GPRs starting either from just the name of the target organism or from an existing metabolic model.
By complementing existing tools for metabolic network reconstruction with the possibility to reconstruct GPRs quickly and with a few resources, GPRuler paves the way to the study of context-specific metabolic networks, representing the active portion of the complete network in given conditions, for organisms of industrial or biomedical interest that have not been characterized metabolically yet.
The documentation to install and use GPRuler is included in the Wiki.
If you use GPRuler in your scientific work, please cite:
Di Filippo M, Damiani C, Pescini D (2021) GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PLoS Comput Biol 17(11): e1009550. doi: 10.1371/journal.pcbi.1009550
For support, please contact Marzia Di Filippo.