This workflow demonstrates the initial steps of a high-throughput screening hitlist triaging workflow: removing molecules that may have interfered with the assay (using the PAINS filters) or that have undesirable physicochemical properties (using the REOS filters).
This is a companion discussion topic for the original entry at https://kni.me/w/7oT-q8X0LGNuz1TH
Personally, when using any substructural alert, I like to do a fisher’s exact test in order to probe the whether any SAR (or SIR, in the case of PAINS…) is tied to that substructure. Otherwise it always feels like throwing the baby away with the bath water. Now, some chemotypes are just garbage and I’ll never progress them nor will any chemist ever work on them. But that is another matter.
Shameless self promotion: https://pubs.acs.org/doi/10.1021/acs.jcim.6b00465