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Bioinformatics Advance Access published online on February 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti295
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received June 11, 2004
Revised January 25, 2005
Accepted January 26, 2005

Letter to the Editor

SuperDrug: a conformational drug database

Andrean Goede 1, Mathias Dunkel 1, Nina Mester 1, Cornelius Frommel 1, and Robert Preissner 1*

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

* To whom correspondence should be addressed.
Robert Preissner, E-mail: Robert.Preissner{at}charite.de


  Abstract

Motivation: Different resources exist for experimentally determined and computed 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 desireable.

Results: The database contains about 2,500 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 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 visualisation.


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