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W3_Unwanted_substructures

Unwanted substructures PAINS TeachOpenCADD
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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). In this workflow, the following steps are presented: 1.Filter out PAINS 2.Filter out unwanted substructures by Brenk et al. 3.Highlight unwanted substructures Author: Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory Landrum, and Andrea Volkamer

External resources

  • Brenk list of unwanted/toxic substructures: Brenk et al.(2008)
  • Pan Assay Interference Compounds (PAINS): Baell et al. (2010)

Used extensions & nodes

Created with KNIME Analytics Platform version 4.5.1 Note: Not all extensions may be displayed.
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    KNIME Base Chemistry Types & Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
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    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
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    RDKit Nodes Feature Trusted extension

    NIBR

    Version 4.5.0

    manuelschwarze
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