Murcko scaffolds with substitution vectors


How can I use the Murcko Scaffold output as input for the R-Group Decomposer? I am looking for a way to see which positions of the Scaffolds are substituted with what.

Tue, 03/20/2012 - 09:45


With the current version you have to convert the output of the Murcko Scaffold Node from a query format to ordinary format: you need to use Indigo To Molecule, and Query Molecule to Indigo nodes sequentially.

I see that it is not very convenient and obvious, and we will try to implement some interface to accept arbitrary formats with automatic conversion.

Tue, 04/24/2012 - 01:18


I've tried the above method but the R-Group Decomposer returns an empty table. The error message is: "Error while decompose molecules: R-Group deconvolution: no embeddings obtained".

Did you succeeded in this operation?

Tue, 04/24/2012 - 05:10


Yes we have resolved the issue with the "R-Group deconvolution: no embeddings obtained" error. The new RGroup Decomposition API was applied for the node and from a next version the incorrect matching will only raise a warning.

The fixed version is almost prepared to be released. I will inform in this topic if the upcoming release is available.

With best regards,


Wed, 04/25/2012 - 08:11