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Interaction Fingerprint Decomposer

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

KNIME node for decomposing an interaction fingerprint into a more human readable overview of interactions (including types) per structure. This node combines the output of the Interaction Types Retriever node and the Interaction Fingerprint Retriever node and decomposes the IFP into a detailed list of kinase-ligand interactions. This node can optionally add the sequence number (according to the structure) and the KLIFS position (e.g. GK.45 for the gatekeeper on position 45) for each pocket residue to the table. It also allows the user to only output interactions that are present (these are encoded as a “1” in the fingerprint) or to output all possible interactions for each residue and indicate whether or not that interaction is observed for a structure. The output of this node allows for example to analyze interaction patterns, to perform association rule learning/pattern recognition, to identify interaction hotspots, and to obtain a detailed overview of kinase-ligand interactions.

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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Table with IFPs and structure IDs
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Output of the Get Interaction Types node

Output Ports

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Decomposed IFP

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install 3D-e-Chem KNIME nodes from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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