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 TSF > 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 


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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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