Hub
Pricing About
WorkflowWorkflow

W3_Unwanted_substructures

Unwanted substructuresPAINSTeachOpenCADD
tymsk3891 profile image
Draft Latest edits on 
Jan 22, 2022 9:24 AM
Drag & drop
Like
Download workflow
Workflow preview
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

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

Used extensions & nodes

Created with KNIME Analytics Platform version 4.5.1 Note: Not all extensions may be displayed.
  • Go to item
    KNIME Base Chemistry Types & NodesTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
  • Go to item
    KNIME Base nodesTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
  • Go to item
    KNIME JavaScript ViewsTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
  • Go to item
    RDKit Nodes FeatureTrusted extension

    NIBR

    Version 4.5.0

    manuelschwarze

Legal

By using or downloading the workflow, you agree to our terms and conditions.

KNIME
Open for Innovation

KNIME AG
Talacker 50
8001 Zurich, Switzerland
  • Software
  • Getting started
  • Documentation
  • Courses + Certification
  • Solutions
  • KNIME Hub
  • KNIME Forum
  • Blog
  • Events
  • Partner
  • Developers
  • KNIME Home
  • Careers
  • Contact us
Download KNIME Analytics Platform Read more about KNIME Business Hub
© 2025 KNIME AG. All rights reserved.
  • Trademarks
  • Imprint
  • Privacy
  • Terms & Conditions
  • Data Processing Agreement
  • Credits