Efficient 3D pharmacophore alignment as a tool for structure-based modeling and scoring

Chemical-feature based pharmacophore models have been established as state-of-the-art technique for bioactivity prediction. While in ligand-based drug design, chemical feature-based pharmacophore creation from a set of bio-active molecules is a frequently chosen approach, structure-based pharmacophores are still lacking the reputation to be an alternative or at least a supplement to docking techniques. Nevertheless, 3D pharmacophore screening bears the advantage of being much more efficient than unattended high-throughput docking and to transparently provide the user with all the information that is used by the screening algorithms to characterize the ligand-macromolecule interaction.