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Similar fragments

3D-e-Chem KNIME KripoDB nodes version 2.5.0.v201909251052 by Netherlands eScience Center

KRIPO stands for Key Representation of Interaction in POckets .

Find similar fragments bound to similar subpockets as the subpocket associated with the query fragment based on the fingerprint similarity matrix.

When combining this node with other Kripo nodes make sure the files are from the same dataset.

The public web service most recent data update was on.

Instead of using the public kripo webservice it is also possible to run a local web service.

Options

Fragment identifiers: The column containing the Kripo fragment identifiers
Cutoff: Cutoff, scores below cutoff are discarded.
Limit: Maximum number of hits for each query.

Advanced Options

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

Input Ports

: Table with Kripo fragment identifiers

Output Ports

: Table with similar Kripo identifiers and scores vs the input table.

Best Friends (Incoming)

MarvinSketch (20 %)
Fragment information (20 %)
Row Filter (20 %) Streamable
Molecule Type Cast (20 %) Streamable
RDKit Molecule Substructure Filter (20 %)

Best Friends (Outgoing)

GroupBy (29 %)
Joiner (29 %)
Fragment information (14 %)
~~Cell Splitter~~ (14 %) Deprecated
Table to PDF (14 %)

Installation

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

KNIME 4.1

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Developers

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