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TeachOpenCADD_​Workflow3_​Unwanted_​substructures

TeachOpenCADD Workflow 3: Molecular filtering: Unwanted Substructures

Compounds can contain unwanted substructures that may cause mutagenic, reactive, or other unfavorable pharmacokinetic effects or that may lead to non-specific interactions with assays (PAINS). Knowledge on unwanted substructures in a dataset can be integrated in cheminformatics pipelines to either perform an additional filtering step before screening or - more often - to set alert flags to compounds being potentially problematic (for manual inspection by medicinal chemists).
This workflow shows how to filter for such unwanted substructures.

With existing node By hand Step 2Filter out unwanted substructures by Brenk et al. This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADDplatform: https://projects.volkamerlab.org/teachopencadd/talktorials/T003_compound_unwanted_substructures.html Step 1Filter out PAINS with existing node Step 3 Highlight unwanted substructures from both sets (PAINS and Brenk) 3. Molecular filtering: unwanted substructuresCompounds can contain unwanted substructures that may cause mutagenic, reactive, or other unfavorablepharmacokinetic effects or that may lead to non-specific interactions with assays (PAINS). Knowledge on unwantedsubstructures in a dataset can be integrated in cheminformatics pipelines to either perform an additional filtering stepbefore screening or - more often - to set alert flags to compounds being potentially problematic (for manual inspection bymedicinal chemists). The following steps show how to filter for such unwanted substructures. With existing node By hand Filter by PAINS Filter by unwanted substructures (Brenk)Filter by unwanted substructures (Brenk)Remove highlightedunwanted substructures columnFilter by unwantedsubstructures (Brenk)List ofunwanted substructuresFlagged moleculesCompounds without PAINS or Brenk flagCompounds with PAINS and/or Brenk flagList of compounds RDKit MoleculeCatalog Filter RDKit MoleculeHighlighting Column Filter RDKit From Molecule Molecule Type Cast Table View RDKit MoleculeSubstructure Filter RDKit MoleculeCatalog Filter Column Filter RDKit MoleculeCatalog Filter Molecule Type Cast RDKit From Molecule CSV Reader Concatenate CSV Writer CSV Writer CSV Reader With existing node By hand Step 2Filter out unwanted substructures by Brenk et al. This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADDplatform: https://projects.volkamerlab.org/teachopencadd/talktorials/T003_compound_unwanted_substructures.html Step 1Filter out PAINS with existing node Step 3 Highlight unwanted substructures from both sets (PAINS and Brenk) 3. Molecular filtering: unwanted substructuresCompounds can contain unwanted substructures that may cause mutagenic, reactive, or other unfavorablepharmacokinetic effects or that may lead to non-specific interactions with assays (PAINS). Knowledge on unwantedsubstructures in a dataset can be integrated in cheminformatics pipelines to either perform an additional filtering stepbefore screening or - more often - to set alert flags to compounds being potentially problematic (for manual inspection bymedicinal chemists). The following steps show how to filter for such unwanted substructures. With existing node By hand Filter by PAINS Filter by unwanted substructures (Brenk)Filter by unwanted substructures (Brenk)Remove highlightedunwanted substructures columnFilter by unwantedsubstructures (Brenk)List ofunwanted substructuresFlagged moleculesCompounds without PAINS or Brenk flagCompounds with PAINS and/or Brenk flagList of compounds RDKit MoleculeCatalog Filter RDKit MoleculeHighlighting Column Filter RDKit From Molecule Molecule Type Cast Table View RDKit MoleculeSubstructure Filter RDKit MoleculeCatalog Filter Column Filter RDKit MoleculeCatalog Filter Molecule Type Cast RDKit From Molecule CSV Reader Concatenate CSV Writer CSV Writer CSV Reader

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: dominique
Created at: 2019-07-15
On NodePit since: 2019-10-03
Last update: 2024-04-20
Created with KNIME version: v4.5.0
Tags: Unwanted substructuresPAINS

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