Journal
NUCLEIC ACIDS RESEARCH
Volume 42, Issue D1, Pages D401-D407Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt1207
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Funding
- Deutsche Forschungsgemeinschaft [DFG] [KU 2796/2-1]
- Novo Nordisk Foundation Center for Protein Research
- European Molecular Biology Laboratory
- Novo Nordisk Foundation Center for Protein Research [PI Lars Juhl Jensen] Funding Source: researchfish
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STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms. Compared with the previous version, the number of high-confidence protein-chemical interactions in human has increased by 45%, to 367 000. In this version, we added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data. For example, a user can now upload a spreadsheet with screening hits to easily check which interactions are already known. To increase the coverage of STITCH, we expanded the text mining to include full-text articles and added a prediction method based on chemical structures. We further changed our scheme for transferring interactions between species to rely on orthology rather than protein similarity. This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files.
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