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MMP FEP input preparation

Protein preparation
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This workflow takes as inputs: a list of PDB structure IDs, corresponding cocrystallized ligand and Matched Molecular Pair smiles. It downloads the biological units, runs the protein-ligand complex preparation and checking. The ligand structures are extracted, the MMP created and the FEP calculation input file generated.

Used extensions & nodes

Created with KNIME Analytics Platform version 4.3.2 Note: Not all extensions may be displayed.
  • KNIME Base Chemistry Types & Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    knime
  • KNIME Core Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    knime
  • KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    knime
  • KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Versions 4.1.0, 4.3.2

    knime
  • RDKit KNIME integration Trusted extension

    NIBR

    Version 4.0.0

    manuelschwarze
  • Schrödinger Extensions for KNIME Trusted extension

    Schrödinger

    Versions 20.1.6, 20.1.9, 20.2.58, 21.3.49

    Schroedinger profile image
    schroedinger
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