Delivering reaction rules to engineer biology
RetroRules is a database of reaction rules for metabolic pathway discovery and metabolic engineering. Reaction rules are generic descriptions of reactions to be used in retrosynthesis workflows in order to enumerate possible biosynthetic routes connecting target molecules to precursors. The use of such rules is becoming more and more important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity.
RetroRules provides a complete set of reaction rules, extracted from public databases and expressed in the community-standard SMARTS format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such multiple representation of reactions expands natural chemical diversity by predicting de novo reactions of promiscuous enzymes. Our rules are readily usable by open source cheminformatics tools such as RDKit as well as more complex retrosynthetic codes such as RetroPath2.0.
Please check the documentation for more details on RetroRules.
RetroRules returns reaction rules to the user by searching through different possible queries such as EC number, reaction ID, substrate structure query...
Please notice that when querying RetroRules, less specific reaction rules are filtered out
according to the
minimal diameter threshold. The diameter is
the sphere including the atoms around the reacting center. The higher is
the diameter, the more specific are the rules. Please have a look to the
documentation for additional details.