Journal of Computer-Aided Molecular Design

, Volume 25, Issue 7, pp 637–647 | Cite as

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

  • Lorenz C. Blum
  • Ruud van Deursen
  • Jean-Louis Reymond


The chemical universe database GDB-13, which enumerates 977 million organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules, represents a vast reservoir for new fragments. GDB-13 was classified using the MQN-system discussed in the preceding paper for the analysis of PubChem fragments. Two hundred and fifty-five subsets of GDB-13 were generated by the combinatorial use of eight restrictive criteria, including fragment-like (“rule of three”) and scaffold-like (no acyclic carbon atoms) filters. Virtual screening for analogs of 15 commercial drugs of 13 non-hydrogen atoms or less shows that retrieving MQN-neighbors of a query molecule from GDB-13 or its subsets provides on average a 38-fold enrichment in structural analogs (Daylight-type substructure fingerprint Tanimoto T SF > 0.7), and a 75-fold enrichment in shape-similar analogs (ROCS TanimotoCombo score > 1.4). An MQN-searchable version of GDB-13 is provided at

Graphical Abstract


Databases Virtual screening Chemical space Enumeration Fragments 



This work was supported financially by the University of Berne, the Swiss National Science Foundation and the Office Fédéral Suisse de l’Education et de la Science.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Lorenz C. Blum
    • 1
    • 2
  • Ruud van Deursen
    • 1
    • 2
  • Jean-Louis Reymond
    • 1
    • 2
  1. 1.Department of Chemistry and BiochemistryUniversity of BerneBerneSwitzerland
  2. 2.Swiss National Center of Competence in Research, NCCR-TransCureUniversity of BerneBerneSwitzerland

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