Ertl Scaffold Keys

This node generates the 32 scaffold keys described by Peter Ertl (" Intuitive Ordering of Scaffolds and Scaffold Similarity Searching Using Scaffold Keys ", Peter Ertl, J. Chem. Inf. Model. 2014, 54 , 1617-1622 and " Identification of Bioisosteric Scaffolds using Scaffold Keys ", Peter Ertl, ChemRxiv , 2021)

The molecules are converted to Murcko-Beamis scaffolds, and descriptors are calculated. The algorithm is implemented using RDKit.

The column properties for the keys show:

We thank Peter Ertl for helpful comments with this node

This node was developed by Vernalis Research (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com

Options

Select molecule column: Select the molecule column (RDKit, SDF, MOL or SMILES format)
Remove input column: Optionally remove the input column
Inputs are Murcko Scaffolds: Check this box if the molecules are already Murcko-Beamis Scaffolds
Depict Keys: If this option is selected then for most keys a depiction column will follow the counts column. Depending on the key, this will be either a single SVG cell for each input row, or a List of SVG cells for each input row
Highlight Colour: The colour to highlight the atoms/bonds contributing to the key. WARNING: Choosing colours with transparency may cause undesired rendering artefacts in the KNIME table

: The molecules with the selected scaffold keys appended. The Murcko-Beamis scaffold is also appended if appropriate.

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To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Vernalis Research, UK

Plugin version: 1.36.7.v202408051613

On NodePit since: 2024-07-11

Last update: 2024-11-21

Tags: Streamable

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4

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