Generation of Murcko Scaffolds and additional ring assembly fragmentation


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.


Solved using ScaffoldGraph in RDKit ScaffoldGraph · PyPI

1 Like

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.

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.