Visualisation and subsets of the chemical universe database GDB-13 for virtual screening |
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Authors: | Lorenz C Blum Ruud van Deursen Jean-Louis Reymond |
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Institution: | (1) Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland;(2) Swiss National Center of Competence in Research, NCCR-TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland; |
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Abstract: | Abstract 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 . |
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Keywords: | |
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