Scaffold hopping is the name for a group of ligand based techniques that seek to discover new ligands starting from existing ligands. There are three classes of such tools: Pharmacophore-based methods, fingerprint based methods and shape based methods.
Scaffold hopping is much used and appreciated in the pharmaceutical industry because it is likely to suggest compounds that are similar to known actives, that have a good chance of being active themselves. In contract, target based methods such as docking tend to produce a much lower rate of actives, but the few that are active are more likely to be really different from what is already known.
Most modern ligand discovery projects use some combination of ligand based and target based techniques.
-- John Irwin