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Oxford University Press, Nucleic Acids Research, D1(40), p. D876-D880, 2011

DOI: 10.1093/nar/gkr1011

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STITCH 3: Zooming in on protein-chemical interactions

Journal article published in 2011 by Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Christian von Mering ORCID, Lars Juhl Jensen ORCID, Peer Bork ORCID,
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/.