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

Blum, Lorenz ; van Deursen, Ruud ; Reymond, Jean-Louis

In: Journal of Computer-Aided Molecular Design, 2011, vol. 25, no. 7, p. 637-647

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    Titel
    • Visualisation and subsets of the chemical universe database GDB-13 for virtual screening
    Autor
    • Blum, Lorenz. Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland
    • van Deursen, Ruud. Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland
    • Reymond, Jean-Louis. Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland
    Dokumententyp
    • Postprint
    Sprache
    • Englisch
    Veröffentlicht in
    • Journal of Computer-Aided Molecular Design, 2011, vol. 25, no. 7, p. 637-647. Springer Netherlands
    Andere elektronische Ausgabe
    OAI-PMH-ID
    • oai:doc.rero.ch:319944
    Summary
    The chemical universe database GDB-13, which enumerates 977million 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 www.gdb.unibe.ch. Graphical Abstract