RetroRules: a database of reaction rules for engineering biology.

Abstract:

RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly 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. Here, we provide for the first time a complete set containing >400 000 stereochemistry-aware reaction rules extracted from public databases and expressed in the community-standard SMARTS (SMIRKS) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such numerous representations of reactions expand natural chemical diversity by predicting de novo reactions of promiscuous enzymes.

SEEK ID: https://hub.ibisba.eu/publications/1

PubMed ID: 30321422

Projects: Uncurated Protocols Library

Publication type: Not specified

Journal: Nucleic Acids Res

Citation: Nucleic Acids Res. 2019 Jan 8;47(D1):D1229-D1235. doi: 10.1093/nar/gky940.

Date Published: No date defined

Registered Mode: Not specified

Authors: T. Duigou, M. du Lac, P. Carbonell, J. L. Faulon

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Created: 23rd Jan 2019 at 09:25

Last updated: 29th Sep 2022 at 13:32

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