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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

Metabolic differences in ripening of Solan... (2)

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Updated data processing workflow for metabolomics LC-MS/MS data. This workflow depends on the stable community plug-in MassCascade and KNIME plug-ins Base Chemistry, Chemistry Types & Nodes, Math Expression, and XLS Support. The workflow was run under KNIME version 2.9.2.

Created: 2013-10-16 | Last updated: 2014-07-04

Credits: SBeisken

Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: Insilicoconsulting

Untargeted metabolomics reveals molecular ... (1)

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Normal 0 false false false EN-US X-NONE AR-SA ...

Created: 2019-06-21

Credits: David_MTX

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

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

Credits: Pablo Carbonell

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: Thomas Duigou BioRetroSynth

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

Texture classification: Knime Image Analytics (1)

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A workflow including image pre-processing and descriptor calculation for building a texture classification model. The workflow can really be used for any kind of image classification task for which has labelled training data.There is significant scope of improvement, both on the image processing , descriptor selection and model building phases..Happy image analytics !

Created: 2015-11-10

Credits: Insilicoconsulting

Pubmed -Google Tag Cloud (1)

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A simple workflow to query PubMed, Google and build a Tag Cloud after some preprocessing.

Created: 2015-11-01

Credits: Insilicoconsulting

Drug-Drug Networks using Matador-DrugBank ... (1)

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These days, Networks of all kinds are all the rage! So here's a trickle contributing to the flood.The workflow generates a network based on Similarity between known drugs based on commonality of their "direct" drug target interactions.The workflow does not provide a comparison between Chemical similarity based network and one based on shared drug targets. It only provides the latter.Other nodes and interfaces to Cytoscape and exported csv can be used to further the network analy...

Created: 2015-09-17 | Last updated: 2015-09-17

Credits: Insilicoconsulting

SAR by Rgroup decomposition (1)

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This workflow showcases a simple way to use Rgroup decomposition for SAR analysis.Once R-groups are obtained for several sites on the Scaffold, molecular properties like logP, TPSA, number of heavy/hetero-atoms, various kinds of ring counts are calculated.While medicinal chemistry purists may decry calculating properties for fragments/R-groups, correlating these at each site with Ki (or activity) shows up interesting trends.It's immediately apparent if increasing logP at a given site incr...

Created: 2015-09-15

Credits: Insilicoconsulting