I've been using KNIME to screen a database of molecules against a certain target compound (substructure search, FTrees, fingerprints...). In the end I obtained a series of SD files. I'd like to merge these files and cluster the molecules based on their core scaffold. Is it possible to classify these structures (approximately 1000 compounds) according to their (central) structure?
In the near future, I'm planning to screen the database of 1000 compounds (from the virtual screen) manually and it would be nice if the structures are arranged in classes.