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: IBISBA Library

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

Help
help Creator
Activity

Views: 303

Created: 23rd Jan 2019 at 10:25

help Attributions

None

Related items

Powered by
(v.1.9.0)
Copyright © 2008 - 2019 The University of Manchester and HITS gGmbH
The Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project is funded by the European Union Horizon 2020 program INFRAIA-02 under grant agreement 730976. The content of IBISBAHub has its own licenses and copyrights