Workflows

Substructure querying | R-group decomposit... (1)

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This workflow creates maximum common substructure (MCS) out of the provided structures and then substructure mining using MCS as a structural query is performed. Obtained hits are then subjected to R-group decomposition to explore their functional groups. Optionally, physicochemical descriptors for individual functional groups can be calculated.

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

Scaffold Analysis | Statistical analysis o... (1)

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This workflow performs an extraction and statistical analysis of Murcko scaffolds for compounds being active against (a) different target(s). Specifically, target-wise detection of Murcko Scaffolds in active versus inactive compounds, filtering steps by removing too generic scaffold (i.e., number of rings equals to one OR number of heteroatoms in a ring is zero or one), calculating the frequency of a particular scaffold which appears frequently in the active over inactive class, applying Fish...

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

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

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

Credits: Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

zetasizer2excel (2)

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Arrrgh! The exported data file format for the Malvern Zetasizer is insane!Row1, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row2, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row3, x1,x2,x3,x4,....,y1,y2,y3,y4,....This workflow imports the txt file, takes each row and reformats as table with 3 columns: Size, Intensity, Volume. Then exports the data for each row to a new tab in Excel. Or you can just use KNIME to plot and prepare reports (to do).The TableRow2Variable node allows you to name the tabs in Excel from a ...

Created: 2017-11-20 | Last updated: 2017-11-20

Credits: sauberns

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

QSAR-model-aminoglycosides (2)

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The workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-iQSAR (2)

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The workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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

QSAR-model-Tg-prediction (2)

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The workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. T...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licen...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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