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Open Access Exploring the Chemical Space of Known and Unknown Organic Small Molecules at

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Organic small molecules are of particular interest for medicinal chemistry since they comprise many biologically active compounds which are potential drugs. To understand this vast chemical space, we are enumerating all possible organic molecules to create the chemical universe database GDB, which currently comprises 977 million molecules up to 13 atoms of C, N, O, Cl and S. Furthermore, we have established a simple classification method for organic molecules in form of the MQN (molecular quantum numbers) system, which is an equivalent of the periodic system of the elements. Despite its simplicity the 42 dimensional MQN system is surprisingly relevant with respect to bioactivity, as evidenced by the fact that groups of biosimilar compounds form close groups in MQN space. The MQN space of the known organic molecules in PubChem and of the unknown molecules in the Chemical Universe Database GDB-13 can be searched interactively using browser tools freely accessible at

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Document Type: Research Article

Affiliations: 1: Department of Chemistry and Biochemistry, NCCR TransCure and NCCR Chemical Biology, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland. [email protected] 2: Department of Chemistry and Biochemistry, NCCR TransCure and NCCR Chemical Biology, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland 3: Biomolecular Screening Facility, NCCR Chemical Biology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

Publication date: November 1, 2011

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  • International Journal for Chemistry and Official Membership Journal of the Swiss Chemical Society (SCS) and its Divisions

    CHIMIA, a scientific journal for chemistry in the broadest sense, is published 10 times a year and covers the interests of a wide and diverse readership. Contributions from all fields of chemistry and related areas are considered for publication in the form of Review Articles and Notes. A characteristic feature of CHIMIA are the thematic issues, each devoted to an area of great current significance.

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