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Bioinformatics Advance Access originally published online on February 2, 2005
Bioinformatics 2005 21(9):1751-1753; doi:10.1093/bioinformatics/bti295
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SuperDrug: a conformational drug database

Andrean Goede {dagger}, Mathias Dunkel {dagger}, Nina Mester , Cornelius Frommel and Robert Preissner *

Berlin Center of Genome Based Bioinformatics, 3D Datamining Group, Institute of Biochemistry Charité, Monbijoustrasse 2, 10117 Berlin, Germany

*To whom correspondence should be addressed.

Motivation: Different resources exist for experimentally determined and computed three-dimensional (3D)-structures of low molecular weight structures but for approved drugs, no free, publicly accessible source of 3D-structures and conformers is available. Furthermore, for selection purposes or 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 would be desirable.

Results: The database contains ~2500 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 105 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.

Availability: For academic use the system is accessible at http://bioinf.charite.de/superdrug. The retrieval system requires the free browser-plugin ‘chime’ from MDL for visualization.

Contact: robert.preissner{at}charite.de


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