RAPID: Randomized pharmacophore identification for drug design

This paper describes a randomized approach for finding invariants in a set of flexible and chemically distinct ligands (drug molecules) that underlies an integrated software system called RAPID currently under development. An invariant is a collection of features embedded in ℝ³ which is present in one or more of the possible low-energy conformations of each ligand. Such invariants are called pharmacophores and contain the parts of the ligand that are primarily responsible for its binding with a receptor. The identification of pharmacophores is crucial in drug design since frequently the structure of targeted receptor is unknown but a number of molecules that interact with it have been discovered by experiments. In these cases the pharmacophore is used as a template for building more effective drugs. It is expected that our techniques and results will prove useful in other applications such as molecular database screening and comparative molecular field analysis.