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Murcko Scaffold

Indigo extensions for KNIME Workbench version 2.0.0.qualifier by EPAM Systems, Inc.

This node calculates Murcko scaffolds of input molecules.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column
The column that contains molecule ctructures.
Append Column
Append a new molecule column (with the name as specified in the text field) if checked, replace the original column otherwise.
Remove terminal 3-rings
Remove 1-substituted rings of size 3.
Remove terminal 4-rings
Remove 1-substituted rings of size 4.
Input type
Treat input as: a molecule.
Treat X as pseudoatom
Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors
Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.

Input Ports

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Table containing a column with molecules.

Output Ports

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The same as input, plus the calculated Murcko scaffolds.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Indigo KNIME integration from the following update site:

KNIME 4.2

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

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Developers

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