Hi everyone,

I have a large hit list (sd file) from a database screening and I'm trying to find out how many members with a specific scaffold are present in my hit list.

I was trying to use the "Align to selected substructure" protocol, however, I had some problems with it.

First of all, it doesn"t find all the molecules with the specific scaffold, and secondly, the number of molecules it finds depends on the molecule I define the substructure in.

Any ideas what the problem is?

Or is there maybe another way of finding molecules with a defined scaffold?

Thanks!