KNIME 3D-e-Chem Contributions version 1.1.2.v201907021300 by 3D-e-Chem
KNIME node to retrieve (a part of) a kinase-ligand complex as a 3D structure in MOL2/PDB format from KLIFS. This node retrieves a set of MOL2/PDB structures from KLIFS based on a user-supplied set of Structure IDs (based on output from the Structures Overview Retriever node). The user can indicate whether to retrieve the full complex, the protein, the pocket, or the ligand. As output the nodes provides a table of structures based on the KLIFS alignment in MOL2/PDB format with the structure ID. As (all structures retrieved from KLIFS are aligned based on the KLIFS pocket definition this node can, for example, be used to compare ligand binding modes, compare protein structures, or to generate structure-based or ligand-based pharmacophores.
To use this node in KNIME, install KLIFS KNIME nodes from the following update site:
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