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Fragment Database FDB-17

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Visini Ricardo, Awale Mahendra, Reymond Jean-Louis,
Project Exploiting and Extending GDB for Drug Discovery
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Original article (peer-reviewed)

Journal JCIM Journal of Chemical Information and Modeling
Volume (Issue) 57(4)
Page(s) 700 - 709
Title of proceedings JCIM Journal of Chemical Information and Modeling
DOI 10.1021/acs.jcim.7b00020

Open Access

Type of Open Access Publisher (Gold Open Access)


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 the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward 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 fragmentlike 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 neighbor search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.