Pharmacophore methods include both target based and ligand based methods for ligand discovery.
Target based pharmacophore methods
Examples of implementation are Insight or Discovery Studio, whereby a 3D stereochemical model of the pharmacophore is derived, either from the receptor properties.
Ligand based pharmacophore methods
A model is inferred from the available known ligands. For instance, the pharmacophore of GPCRs such as dopamine, beta2 adrenergic, and histimine, are simply, to a first approximation, based on the presence of charged amine, aromatic ring, and hydroxyl groups present in these molecules. Obvviously much more sophisticated methods are available.
Of course, if both ligand and target information is available, it may be possible to combine information from both sources to build a better model.
-- John Irwin