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Standardization workflow for Mass Spectrometry chemical structures pretreatment.

QSAROPERAStandardizationTautomersPrediction
kmansouri profile image
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Jan 28, 2014 8:07 PM
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Performs required structure standardization tasks (related to salts/solvents, tautomers/mesomers, mixtures, inorganics, metals, aromaticity, 2D/3D...) prior to MS related data analysis. Starts from structures in SDF or SMILES format and produces standardized structures in different formats based on the selected parameters. It also provides the list of failed structures and a summary file with initial and MS-ready smiles as well as InChI and InChIKeys. 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: McEachran, A.D., Mansouri, K., Grulke, C. et al. “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies. J Cheminform 10, 45 (2018). https://doi.org/10.1186/s13321-018-0299-2

External resources

  • KNIME Hub
  • GitHub repository
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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 FeatureTrusted 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 & NodesTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    KNIME Base nodesTrusted extension

    KNIME AG, Zurich, Switzerland

    Versions 4.1.1, 4.5.1

    knime
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    KNIME Excel SupportTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.1

    knime
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    KNIME JavasnippetTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    KNIME Math Expression (JEP)Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    KNIME Quick FormsTrusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.5.0

    knime
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    Vernalis KNIME NodesTrusted extension

    Vernalis Research Ltd, Cambridge, UK

    Version 1.30.3

    vernalis

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