title: The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
abstract: A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.affiliation: Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA.
authors.forename: John H
authors.initials: JH
authors.lastname: Morris
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
authors.forename: Helen
authors.initials: H
authors.lastname: Cook
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kuhn
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wyder
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Milan
authors.initials: M
authors.lastname: Simonovic
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
authors.forename: Nadezhda T
authors.initials: NT
authors.lastname: Doncheva
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Roth
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany bork@embl.de.|Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.|Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.|Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark lars.juhl.jensen@cpr.ku.dk.
authors.forename: Lars J
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland mering@imls.uzh.ch.
authors.forename: Christian
authors.identifier: 0000-0001-7734-9102
authors.initials: C
authors.lastname: von Mering
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D011506:Proteins