Pharmacophore Mapping And Drug Design
A very important part of drug design is prediction of small molecule binding to a target macromolecule. A reasonable qualitative prediction of binding can be made by specifying the spatial arrangement of a small number of atoms or functional groups. Such arrangement is called pharmacophore. The pharmacophore search finds molecules with different overall chemistries, but which have the functional groups in the correct geometry. A common use of pharmacophores is to search 3D databases for molecules that contain the pharmacophore.