myExperiment - Workflows

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Tag: metabolic network

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KNIME

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Thomas Duigou

RetroPath2.0 - a retrosynthesis workflow w... (15)

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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: 2022-02-24

Credits: Thomas Duigou Baudoin Delépine BioRetroSynth

Pipeline Pilot

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Paul Dobson

M5 Charge Matching (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.

Created: 2010-06-03

Credits: Paul Dobson

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Paul Dobson

M4 Tautomer Matching (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.

Created: 2010-06-03

Credits: Paul Dobson

Pipeline Pilot

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Paul Dobson

M3 Non-stereo Matching (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.

Created: 2010-06-03

Credits: Paul Dobson

Pipeline Pilot

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Paul Dobson

M2 Similarity Matching (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.

Created: 2010-06-03

Credits: Paul Dobson

Pipeline Pilot

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Paul Dobson

M1 Exact Matching (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.

Created: 2010-06-03

Credits: Paul Dobson

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Paul Dobson

C1 Combined Workflow (1)

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The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.

Created: 2010-06-03 | Last updated: 2010-06-03

Credits: Paul Dobson

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