STITCH is a database of known and predicted interactions between chemicals and proteins. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases. STITCH data is derived from 5 main sources: Genomic context predictions, High-throughput lab experiments, Conserved co-expression, Automated textmining, previously published knowledge in databases.
- STITCH data is based on STRING data.
- You can search for individual proteins, protein families (using COGs) and chemical structures (using SMILES strings).
- In the "Settings" tab you can choose whether your network edges (which represent the predicted associations) are shown as type of evidence, confidence strengths, predicted molecular actions, or binding affinities. This is also where you adjust your confidence limit and choose which types of evidence you want to use in your search (for example, you can exclude textmining evidence).
- The default view of your search is of the interaction network but much more information can be gathered by switching your viewer, clicking on nodes and edges, exploring the "Legend" and "Analysis" tabs, etc (see "STICH Help" page).
- Beware of the association with Selenomethionine that often comes up if their is a structure.
This website can be used to quickly and easily gather a wide range of information.
When using STITCH, please consult (and cite) any of the following references:
- Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4.
- Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7.
- Kuhn M, Szklarczyk D*, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80.
- Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res. 2010 Jan;38(Database issue):D552-6.
- Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8.