Pharmacophore modeling and three-dimensional database searching for drug design using catalyst

Perceiving a pharmacophore is the first essential step towards understandin g the interaction between a receptor and a ligand. Once a pharmacophore is established, a beneficial use of it is 3D database searching to retrieve no vel compounds that would match the pharmacophore, without necessarily dupli cating the topological features of known active compounds thence remain ind ependent of existing patents). As the 3D searching technology has evolved o ver the years, it has been effectively used for lead optimization, combinat orial library focusing, as well as virtual high-throughput screening. Clear ly established as one of the successful computational tools in rational dru g design, we present in this review article a brief history of the evolutio n of this technology and detailed algorithms of Catalyst(TM), the latest 3D searching software to be released. We also provide brief summary of publis hed successes with this technology, including two recent patent application s.