Murcko scaffold generation

Hi all,





I was looking for a while now already if and how there as an easy way to get just the scaffolds of a library. I am aware that one can easily get the set of rings (e.g., a SMARTS that removes all non-ring atoms), but I also want to have the linkers in between attached to them (with inclusion of exocyclic/exolinker double-bonded atoms).





Is this functionality already integrated somewhere? Would be nice to have it perhaps as an option from Standardizer (even though strictly speaking it isn't standardizing...) or in Fragmenter.





Thanks a lot,





Florian

Hi Florian,





have you come across our LibraryMCS software? I reckon it does just what you need: picks all scaffolds common to subsets of the library and clusters the structures with respect to these scaffolds in a hierarchical manner.





You may wish to try it online at http://www.chemaxon.com/shared/libMCS/.





I am not sure though that such functionality will be included in Standardizer or other tools. We rather aim to make these components available as KNIME (PP, etc) nodes, as well as web services. Would these solutions be appropriate for you?





Regards,


Miklos