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Standardization workflow for QSAR-ready chemical structures pretreatment.

QSAR OPERA Standardization Tautomers Prediction
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Performs required structure standardization tasks (related to salts/solvents, tautomers/mesomers, mixtures, inorganics, metals, aromaticity, 2D/3D...) prior to QSAR modeling or prediction. Starts from structures in SDF or SMILES format and produces standardized structures in different formats based on the selected parameters: - Dimensions: 2D/3D - Rings: Kekule or aromatic - Format: SDF/SMILES It also provides the list of failed structures and a summary file with initial and QSAR-ready smiles as well as InChI and InChIKeys. The parameters selected by default are suggested for use in OPERA. All configuration required is available in the input component. The workflow will then adapt and run autonomously. The workflow can also be executed in batch mode using the command line: <knime path>\knime.exe -reset -nosplash -nosave -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="knime-workspace/QSAR-ready_2.5.8" -workflow.varaiable=cmd_input,"<input path>\inputfile",String Reference: Mansouri, K., Grulke, C.M., Judson, R.S. et al. OPERA models for predicting physicochemical properties and environmental fate endpoints. J Cheminform 10, 10 (2018). https://doi.org/10.1186/s13321-018-0263-1

External resources

  • GitHub repository
  • KNIME Hub

Used extensions & nodes

Created with KNIME Analytics Platform version 4.5.1 Note: Not all extensions may be displayed.
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    ChemAxon/Infocom Marvin Extensions Feature Trusted extension

    Infocom Corporation

    Versions 4.0.0, 4.4.0

    infocom
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    Indigo KNIME integration

    EPAM Systems, Inc.

    Version 2.0.0

    epam-lsop
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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

    Versions 4.1.1, 4.5.1

    knime
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    KNIME Excel Support Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Versions 4.1.0, 4.5.0

    knime
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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    RDKit Nodes Feature Trusted extension

    NIBR

    Version 4.5.0

    manuelschwarze
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    Vernalis KNIME Nodes Trusted extension

    Vernalis Research Ltd, Cambridge, UK

    Version 1.30.3

    vernalis
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