NAR Molecular Biology Database Collection entry number 902
Goede, A.1, Dunkel, M.1, Mester, N.1, Preissner, R.1
1Berlin Center of Genome Based Bioinformatics, 3D Datamining Group Institute of Biochemistry, Charité - University Medicine Berlin, Monbijoustr. 2, 10117 Berlin Germany

Database Description

The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. For selection purposes and for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemical (ATC) classification codes to each structure according to the WHO-scheme is applied. To account for structural flexibility they are represented by 10(5) structural conformers. Here we present a web-query
system enabling searches for drug name, synonyms, trade name, trivial name, formula, CAS-number, ATC-code etc. 2D-similarity screening (Tanimoto coefficients) and an automatic 3D-superposition procedure based on conformational representation are implemented. Drug structures above a similarity threshold as well as superimposed conformers can be retrieved in the mol-file format via a graphical interface.


This work is supported by the BMBF funded Berlin Center for Genome Based Bioinformatics (BCB).


1. A. Goede; M. Dunkel; N. Mester; C. Frommel; R. Preissner, Bioinformatics, 2005, 21, 1751-1753.
2. M. Thimm; A. Goede; S. Hougardy; R. Preissner, J Chem Inf Comput Sci, 2004, 44, 1816-1822.
3. S. Lorenzen; M. Dunkel; R. Preissner, Biosystems, 2005, 80, 117-122.
4. E. Michalsky; M. Dunkel, A. Goede; R. Preissner, BMC Bioinformatics, 2005, 6, 122.
5. M. Fullbeck; X. Huang; R. Dumdey; C. Frommel; W. Dubiel; R. Preissner, BMC Cancer, 2005, 5, 97.
6. WHO, The selection and use of essential medicines. World Health Organ TechRep. Ser., 2004, 920, 1-127.

Subcategory: Small molecules
Subcategory: Drugs and drug design

Go to the abstract in Bioinformatics, 2005, 21, 1751-1753
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