RAPID: Randomized Pharmacophore Identification for drug design

P. W. Finn, L. E. Kavraki, J.-C. Latombe, C. Shelton, S. Venkat, and A. Yao, “RAPID: Randomized Pharmacophore Identification for drug design,” Computational Geometry: Theory and Applications, vol. 10, no. 4, pp. 263–272, 1998.


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 Image3 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.

Publisher: http://dx.doi.org/10.1016/S0925-7721(98)00008-X

PDF preprint: http://kavrakilab.org/publications/finn-kavraki1998rapid-randomized-pharmacophore.pdf