STRING: known and predicted protein–protein associations, integrated and transferred across organisms

By C. von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, M. Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork. Nucleic Acids Res., 2004

1,723 citations recorded by the source corpus.

A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical binding, but can also mean indirect interaction such as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive, yet quality-controlled collection of protein–protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable. STRING currently holds 730 000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/830fdb7b17cfa7b96693c41f04416c05ccbf34e6

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Citations in the corpus

STRING 7—recent developments in the integration and prediction of protein interactions (2006, methodology): “STRING systematically executes such orthology transfers, using both precomputed orthologs from the COG database (20), as well as a homology-based orthology scheme computed de novo ( 11 ).”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, methodology): “In the past, STRING has therefore used two distinct heuristic options: either to substitute homology for orthology (46) or to use pre-defined orthology relations described at high-level taxonomic groups, from the COG database (47).”
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, background): “Understanding PPI network evolution across different species is an important problem [10-13].”
Extracting interactions between proteins from the literature (2008, neutral): “It focuses on experimentally verified protein interactions with special emphasis on proteomes from mammalian organisms mint.bio.uniroma2.it/mint STRING STRING, a database consisting of known and predicted protein–protein interactions, quantitatively integrates interaction data from several sources f”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “For instance, whereas we used BLAST-BDBHs as criteria to detect orthologs between pairs of genomes, STRING uses COG-based definitions of orthology, whereas PROLINKS uses one-way BLAST hits (not necessarily orthologs).”
SMART 5: domains in the context of genomes and networks (2005, methodology): “This information is imported from the STRING database (7), in which known and predicted protein–protein associations are integrated from a variety of sources.”
STITCH: interaction networks of chemicals and proteins (2007, background): “Chemical–protein interactions are transferred between species based on the sequence similarity of the proteins (26).”
Systematic discovery of in vivo phosphorylation networks. (2007, methodology): “In the second stage, the contextforeachsubstrateisrepresentedbyaprobabilistic protein network extracted from the STRING database (von Mering et al., 2005), which integrates information from curated pathway databases, cooccurrence in abstracts, physical protein interaction assays, mRNA expression…”