Bemis Murcko Clustering

[Andrew Orry]

Q. How to perform Bemis Murcko chemical clustering https://pubmed.ncbi.nlm.nih.gov/8709122/?

A. 

We do not have this exact method but you can simulate something similar by combining short small ecfp fingerprints with detailed atom types combined with larger topological ones which ignore atom type and use hybridization and ring/chain properties. This will "catch" common scaffold properties plus some local specific groups.

There is not GUI for that. Command line may look like this: (assuming input table name is 't')

# add column with combo fingeprints
add column t name="fp" Descriptor( t.mol Collection("ATMAP" {"cd,h","sp"} "SIZE" 2048 "BOMAP" { "bt" "r" } "LEN" {4 12} "TYPE" "ecfp") )
# tree clustering by this column
make tree t full "UPGMA" split="cl" name="" column={"fp"}