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Tag: metabolism
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Workflow 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: User Thomas Duigou User Baudoin Delépine Network-member BioRetroSynth

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Workflow Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

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Workflow Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

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Workflow Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

Workflow Count the number of MetaPrint2D predicted ... (1)

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 MetaPrint2D (doi: 10.1186/1471-2105-11-362) is used to calculate the number of red, orange, and green markers that indicate how likely an atom in the drug is metabolized (read the paper for the fine prints). It counts them for each molecule and reports them, as a set of three molecular descriptors that could potentially correlate with how well the molecule is metabolized (hypothesis).

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: User Egon Willighagen

Workflow M5 Charge Matching (1)

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: User Paul Dobson

Workflow M4 Tautomer Matching (1)

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: User Paul Dobson

Workflow M2 Similarity Matching (1)

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: User Paul Dobson

Workflow M1 Exact Matching (1)

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: User Paul Dobson

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