title: STITCH 3: zooming in on protein-chemical interactions.
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/.
authors.affiliation: Biotechnology Center, TU Dresden, 01062 Dresden, Germany. bork@embl.de
authors.forename: Michael
authors.initials: M
authors.lastname: Kuhn
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.forename: Andrea
authors.initials: A
authors.lastname: Franceschini
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D001669:Biochemical Phenomena; D030562:Databases, Protein; D004364:Pharmaceutical Preparations / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D787-91
references.pmid: 19933260
references.citation: PLoS Comput Biol. 2011 May;7(5):e1002043
references.pmid: 21573205
references.citation: Mol Syst Biol. 2010 Dec 21;6:451
references.pmid: 21179023
references.citation: Bioinformatics. 2006 Mar 15;22(6):645-50
references.pmid: 16046493
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9
references.pmid: 19850718
references.citation: PLoS Comput Biol. 2010 Sep 09;6(9):
references.pmid: 20838579
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D552-6
references.pmid: 19897548
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
references.pmid: 21045058
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22
references.pmid: 17942422
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D673-7
references.pmid: 16381956
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41
references.pmid: 21059682
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8
references.pmid: 18084021
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Nat Rev Genet. 2006 Feb;7(2):119-29
references.pmid: 16418747
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92
references.pmid: 18782832
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references.pmid: 19880382
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7
references.pmid: 21067998
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):412-5
references.pmid: 11752352
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33
references.pmid: 19498078
references.citation: J Chem Inf Model. 2011 Jul 25;51(7):1593-603
references.pmid: 21644501
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7
references.pmid: 21948594
references.citation: Mol Syst Biol. 2010;6:343
references.pmid: 20087340
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51
references.pmid: 21097890
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D198-201
references.pmid: 17145705
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6
references.pmid: 18048412