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Nucleic Acids Research Advance Access published online on December 15, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm795
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

STITCH: interaction networks of chemicals and proteins

Michael Kuhn1, Christian von Mering2, Monica Campillos1, Lars Juhl Jensen1,* and Peer Bork1,3

1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland and 3Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany

*To whom correspondence should be addressed. Tel: +49 6221 387 296; Fax: +49 6221 387 519; Email: jensen{at}embl.de Correspondence may also be addressed to Peer Bork. Tel: +49 6221 387 526; Fax: +49 6221 387 519; Email: bork{at}embl.de

Received August 14, 2007. Revised September 14, 2007. Accepted September 17, 2007.

The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH (‘search tool for interactions of chemicals’) integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug–target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/


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