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Structures Retriever

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.

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 structure 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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