Pharmacophore and physico-chemical property-colored fragmental descriptors 

Both fragment counts and pharmacophore pattern fingerprints are classical, well-established molecular descriptors, thought to be complementary. The former provide a molecular skeleton-dependent encoding of the main substructures, while the latter capture information about relative spatial distributions of pharmacophore groups and are less focused on how these are interconnected (thus prone to successful lead hopping). We now set to explore hybrid intermediates of these two extreme classes of descriptors, such as pharmacophore fragments (substructures of the pharmacophore feature-colored molecular graph, having atom symbols replaced by their types) – all while benefiting from the pH-dependent flagging scheme achievable by means of the ChemAxon microspecies calculator. Alternatively, atom coloring by their partial charge, using the ChemAxon charge plugin, will be explored. Examples of usage of these descriptors in QSAR and similarity searches will be shown.