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W3_​Unwanted_​substructures

W3_Unwanted_substructures
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. Step 1Filter out PAINS with existing node Step 2Filter out unwanted substructures by Brenk et al. With existing node By hand Step 3 Highlight unwanted substructures from both sets (PAINS and Brenk) 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 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 flagNode 281Node 282Node 283Node 284 RDKit MoleculeCatalog Filter RDKit MoleculeHighlighting Column Filter 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 RDKit From Molecule WorkflowService Input CSV Reader WorkflowService Output WorkflowService Output 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. Step 1Filter out PAINS with existing node Step 2Filter out unwanted substructures by Brenk et al. With existing node By hand Step 3 Highlight unwanted substructures from both sets (PAINS and Brenk) 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 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 flagNode 281Node 282Node 283Node 284 RDKit MoleculeCatalog Filter RDKit MoleculeHighlighting Column Filter 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 RDKit From Molecule WorkflowService Input CSV Reader WorkflowService Output WorkflowService Output

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Created by: tymsk
Created at: 2022-01-22
On NodePit since: 2022-01-28
Last update: 2024-05-02
Created with KNIME version: v4.5.1
Tags: Unwanted substructuresPAINSTeachOpenCADD

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