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Structures Overview Retriever

KNIME 3D-e-Chem Contributions version 1.1.2.v201907021300 by 3D-e-Chem

KNIME node to retrieve a list of structure IDs from KLIFS of structures in complex with specific kinases (kinase IDs) or ligands (ligand IDs). A user-supplied set of KLIFS kinase IDs (from the Kinase Information Retriever or Kinase ID Mapper node) or KLIFS ligand IDs (from the Ligands Overview Retriever node) can be used to retrieve a list of structures from specific kinases or structures in complex with specific ligands. This allows, for example, to obtain a list of kinase structures that are in complex with ligand that match a specific substructure or to obtain a list of all structures from a specific kinase family. This node returns the structure ID, kinase name, kinase ID, PDB-code, chain, alternate model, RMSD1, RMSD2, the amino acid sequence of the pocket based on the structure, the resolution, the quality of the structure, the number of missing residues, the number of missing atoms, the allosteric ligand, the orthosteric ligand, the allosteric ligand, the conformation of the DFG-motif, the conformation of the αC-helix, the distance, angle and rotation of the G-rich loop, and whether or not the ligand targets the front pocket, the gate area, the back pocket, and the subpockets FP-I, FP-II, BP-I-A, BP-I-B, BP-II-in, BP-II-A-in, BP-II-B-in, BP-II-out, BP-II-B, BP-III, BP-IV, and BP-V.

Options

Advanced Options

Base path
Url to use as base path for KLIFS webservice
Timeout
Timeout in seconds to wait for KLIFS webservice response

Input Ports

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Input with at least a column with kinase IDs

Output Ports

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All structural information obtained from KLIFS

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KLIFS KNIME nodes from the following update site:

KNIME 4.3

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Developers

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