Generation of Murcko Scaffolds and additional ring assembly fragmentation

Groups Cheminformatics
1

Hi,

I would like to create a Workflow that generates Scaffolds from an SDF input file.

The steps would be:

  • Murcko fragments
  • Further fragmentation generating the following scaffold types
  • Contiguous ring systems
  • Contiguous ring systems that share two or more bonds (bridges between rings)

With the Indigo “Murcko Scaffold” node, I was able to generate Murcko scaffolds with the expected outcome but so far I was not able to reproduce further ring system fragmentation with the available fragmentation nodes (e.g. Vernalis) that resulted in the expected outcome.

I attached an image with molecules expected. It would be nice if someone has an idea on implementing this in KNIME. I also will try if I can achieve this with RDKit + Python but have not done this in the past so if someone can give me a hint using the RDKit tool would also be very nice.

Many thanks in advance.

Best

Murcko_RA_fragments
Murcko_RA_fragments1813×1050 106 KB

2

Solved using ScaffoldGraph in RDKit ScaffoldGraph · PyPI

1 Like
3

I was just coming to point you to the RDKit’s own scaffold network implementation (some documentation here: RDKit: Interactively exploring ScaffoldNetwork options).

Glad you found something that works for you; I should also check out ScaffoldGraph at some point to see if there’s anything we should consider bringing into the RDKit core.
-greg

4

Hi Greg, many thanks for your reply. This is great actually. With ScaffoldGraph I was still not able to include scaffolds that consist of tow or more rings that are connected via bridge-atoms of a certain length.

Best

A.