Diversity space and its application to library selection and design

To promote more productive combinatorial endeavors, the Diversity Space methodology introduced here enables similarity comparisons at the library level. Particularly at an early screening stage, when little or no information is available regarding the pharmacophoric entities necessary for binding, it is more efficient to select or discard an entire ensemble of molecules at once, rather than focus on individual compounds. Also described are applications of the methodology to a form of scaffold hopping, herein categorized as soft scaffold hopping, and to a newly introduced approach called surrogate synthesis, both of which are furthered by library-level information that is absent in more traditional molecular similarity calculations.