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Tag: workflow Group: BioRetroSynth

Workflow RetroPath2.0 - a retrosynthesis workflow w... (6)

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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 l...

Created: 2017-05-24 | Last updated: 2018-07-30

Credits: User Baudoin Delépine Network-member BioRetroSynth

Workflow KNIME Workflow for RetroRules and Retropat... (3)

KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: User Pablo Carbonell

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Workflow RetroPath2.0-Mods-isomer-transformation-queue (2)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.4.1 of Kni...

Created: 2017-10-12 | Last updated: 2017-12-19

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data Workflow RetroPath2.0-Mods-isomer-transformation

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