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.

Quick start

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.

► Search by EC number

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Find reaction rules that are related to an EC number.

► Search by reaction ID

Find reaction rules that are specific to a reaction.

► Search by substrate name

Find reactions rules generated from reaction using a specified compound as substrate.

► Search by substrate structure

Find reactions rules generated from reaction using specified InChI as substrate.

To obtain InChI depictions, you can either browse metabolic databases or draw the compound using PubChem Sketcher and converting it to InChI (by choosing "StdInChI" in the menu at the top).