This article is part of the supplement: 5th German Conference on Cheminformatics: 23. CIC-Workshop

Poster presentation

Where are the boundaries? Automated pocket detection for druggability studies

Andrea Volkamer^1*, T Grombacher² and Matthias Rarey¹

• * Corresponding author: Andrea Volkamer

Author Affiliations

¹ University of Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany

² Bioinformatics, Merck Serono, Frankfurter Str. 250, 64293 Darmstadt, Germany

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Journal of Cheminformatics 2010, 2(Suppl 1):P11 doi:10.1186/1758-2946-2-S1-P11

Published: 4 May 2010

First paragraph (this article has no abstract)

Computer-based prediction of protein druggability is an essential task in the drug development process. Early identification of disease modifying targets that can be modulated by low-molecular weight compounds can help to speed up and reduce costs in drug discovery. Recently, first methods have been presented performing a druggability estimation solely based on the 3D structure of the protein [1-3]. The essential first step for such methods is the identification of the active site. A multitude of methods exist for automated active site prediction [4-6]. However, most methods developed for automated docking procedures do not explicitly focus on the definition of the boundary of the active site. Since druggability estimates are based on structural descriptors of the active site, a precise description of the active site boundaries is vital for correct predictions.