NP fragment library. This was generated for use in fragment based drug discovery (FBDD), with a focus on practical application and commercial fragment availability. Although not originally intended to be used for statistical analysis of NP characteristics, it is used as such here because it forms the basis of the PNP classification algorithm. The library was assembled starting from 183,769 NPs containing at least one ring, which contained 110,485 fragments. Using pharmacophore, physical property and chemical alert filtering, this was reduced to 2000 representative clusters and further refined to a set of Murcko scaffold fragments. The NP library is composed of 1673 fragments (MW 42-294) having either single ring systems (1421 fragments) or >1 ring system (252 fragments). Because of its targeted makeup, small size, and property distribution, the fragment NP library lacks NP acyclic substituents and there is no directly comparable 'non-NP' fragment set that could be used as a control set. Representation of all NP chemical ring systems is an impractical proposition. For example, other similar studies found 134,102 fragments (MW 100-300) including acyclic moieties in a set of 210,213 NPs, and 38,662 unique ring systems were found in 269,226 NPs, of which 23,299 (60%) were singletons. High diversity is apparent in studies of scaffold occurrence: singleton scaffolds dominate the medicinal chemistry literature and only 763 of 103,772 scaffolds (0.7%) in the ChEMBL 20 database were found in >10 compounds. Not surprisingly, high proportions of singleton NP fragments, and singleton NP fragment combinations, are also seen in the Clinical and Reference compound sets (see Results). Of the 30 most abundant NP ring systems reported, 21 passed the fragment filtering process applied and are present in the NP fragment library.