The process for developing a pharmacophore model generally involves the following steps:
# Select a training set of ligands – Choose a structurally diverse set of molecules that will be used for developing the pharmacophore model. As a pharmacophore model should be able to discriminate between molecules with and without bioactivity, the set of molecules should include both active and inactive compounds.
# Conformational analysis – Generate a set of low energy conformations that is likely to contain the bioactive conformation for each of the selected molecules.
#Molecular superimposition – Superimpose ("fit") all combinations of the low-energy conformations of the molecules. Similar (bioisosteric) functional groups common to all molecules in the set might be fitted (e.g., phenyl rings or carboxylic acid groups). The set of conformations (one conformation from each active molecule) that results in the best fit is presumed to be the active conformation.
#Abstraction – Transform the superimposed molecules into an abstract representation. For example, superimposed phenyl rings might be referred to more conceptually as an aromatic ring pharmacophore element. Likewise, hydroxy groups could be designated as a hydrogen-bond donor/acceptor pharmacophore element.
# Validation – A pharmacophore model is a hypothesis accounting for the observed biological activities of a set of molecules that bind to a common biological target. The model is only valid insofar as it is able to account for differences in biological activity of a range of molecules.
As the biological activities of new molecules become available, the pharmacophore model can be updated to further refine it.