RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

Created: 2017-05-24 12:50:16      Last updated: 2022-02-24 15:12:01

The RetroPath2.0 workflow build a reaction network from a set of source compounds to a set of sink compounds.

When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively link a source to a subset of sink compounds. This sub-network is considered as a scope and is output in dedicated files (see below).

The workflow handles both monomolecular (1 substrate) and bimolecular (2 substrates) reactions.

Getting started
See instructions in RetroPath2.0_tutorial file.

Usage specifications
RetroPath2.0 workflow is compatible up to version 3.6.2 of the KNIME Analytics Platform.

Limitations as of 2019/10/07
Scope is only relevant for retrosynthetic usage (target/source to chassis/sink).

Release: r20191007

How to cite
Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering (2018). DOI:

Please report bugs to

Worfklow Licence: GNU General Public License v3.0
T Duigou, B Delépine, JL Faulon, 2017-2019. This work is licensed under the GNU General Public License v3.0. To view a copy of the license please visit

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