Reymond Research Group

University of Bern

Fragment Database FDB-17

The paper Fragment Database FDB-17 has been accepted for publication in the Journal of Chemical Information and Modeling.

To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following simple rules of chemical stability and synthetic feasibility. However due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased towards the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragment-like molecules evenly covering a broad value range for molecular size, polarity and stereochemical complexity. The database is available at for download and free use, together with an interactive visualization application and a web-based nearest neighbour search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.

Author(s): Ricardo Visini, Mahendra Awale and Jean-Louis Reymond