RAPID: randomized pharmacophore identification for drug design

This paper describes a randomized approach for finding invariants in a set of flexible ligands (drug molecules) that underlies an integrated software system called RAPID currently under development. An invariant is a collection of features embedded in 3 which is present in one or more of the possible low-energy conformations of each ligand. Such invariants of chemically distinct molecules are useful for computational chemists since they may represent candidate pharmacophores. A pharmacophore contains the parts of the ligand that are primarily responsible for its interaction and binding with a specific receptor. It is regarded as an inverse image of a receptor and is used as a template for building more effective pharmaceutical drugs. The identification of pharmacophores is crucial in drug design since the structure of the targeted receptor is frequently unknown, but a number of molecules that interact with the receptor have been discovered by experiments. It is expected that our techniques and the results produced by our system will prove useful in other applications such as molecular database screening and comparative molecular field analysis.

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