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J Chem Inf Model. 2012 Nov 26;52(11):2864-75. doi: 10.1021/ci300415d. Epub 2012 Nov 1.

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.

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Department of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.


Drug molecules consist of a few tens of atoms connected by covalent bonds. How many such molecules are possible in total and what is their structure? This question is of pressing interest in medicinal chemistry to help solve the problems of drug potency, selectivity, and toxicity and reduce attrition rates by pointing to new molecular series. To better define the unknown chemical space, we have enumerated 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens forming the chemical universe database GDB-17, covering a size range containing many drugs and typical for lead compounds. GDB-17 contains millions of isomers of known drugs, including analogs with high shape similarity to the parent drug. Compared to known molecules in PubChem, GDB-17 molecules are much richer in nonaromatic heterocycles, quaternary centers, and stereoisomers, densely populate the third dimension in shape space, and represent many more scaffold types.

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