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Melchior Du Lac

About Melchior Du Lac:

Computational Biologist

SEEK ID: https://hub.ibisba.eu/people/106

Location:  France

Expertise: Workflows, Kinetic modelling, Bacterial Cell Cycle

Tools: C, Cytometry and fluorescent microscopy, Python, FBA, Java

ORCID: https://orcid.org/0000-0002-9984-4689

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Programme: IBISBA

Public web page: http://www.ibisba.eu

Muconic acid production

Construction of a P. putida KT2440 producing cis,cis-muconate from glucose, benzoate, or p-coumarate

Programme: IBISBA

Public web page: Not specified

Start date: 3rd Nov 2017

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RetroRules: a database of reaction rules for engineering biology.
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Abstract (Expand)

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.

Authors: Thomas Duigou, Melchior Du Lac, P. Carbonell, Jean-Loup Faulon

Date Published: No date defined

Journal: Nucleic Acids Res

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