Resource Citation
The UniProt Consortium
UniProt: the universal protein knowledgebase in 2021
Nucleic Acids Res. 49:D1 (2021) Samaras et al., ProteomicsDB: a multi-omics and multi-organism resource for life science research. Nucleic Acids Res. 2019 Oct 30
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 Szklarczyk D*, Gable AL*, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P‡, Jensen LJ‡, von Mering C‡.
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets .
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-12.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P‡, Jensen LJ‡, von Mering C‡.
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res. 2019 Jan; 47:D607-613.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P‡, Jensen LJ‡, von Mering C‡.
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Nucleic Acids Res. 2017 Jan; 45:D362-68.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P‡, Jensen LJ‡, von Mering C‡.
STRING v10: protein-protein interaction networks, integrated over the tree of life.

Nucleic Acids Res. 2015 Jan; 43:D447-52.

Franceschini A, Lin J, von Mering C, Jensen LJ‡.
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.
Bioinformatics. 2015 Nov; btv696.

Franceschini A*, Szklarczyk D*, Frankild S*, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P‡, von Mering C‡, Jensen LJ‡.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Nucleic Acids Res. 2013 Jan; 41:D808-15.

Szklarczyk D*, Franceschini A*, Kuhn M*, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P‡, Jensen LJ‡, von Mering C‡.
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Nucleic Acids Res. 2011 Jan; 39:D561-8.

Jensen LJ*, Kuhn M*, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P‡, von Mering C‡.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res. 2009 Jan; 37:D412-6.

von Mering C*, Jensen LJ*, Kuhn M, Chaffron S, Doerks T, Krueger B, Snel B, Bork P‡.
STRING 7--recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res. 2007 Jan; 35:D358-62.

von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P‡.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res. 2005 Jan; 33:D433-7.

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P‡, Snel B.
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Res. 2003 Jan; 31:258-61.

Snel B‡, Lehmann G, Bork P, Huynen MA.
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Nucleic Acids Res. 2000 Sep 15;28(18):3442-4.

*contributed equally
‡corresponding author
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Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P, Vidal M. Next-generation sequencing to generate interactome datasets. Nat Methods. 2011 Jun;8(6):478-80. doi: 10.1038/nmeth.1597. Epub 2011 Apr 24. PMID: 21516116; PMCID: PMC3188388.

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 Jumper, J et al. Highly accurate protein structure prediction with AlphaFold (Nature 2021). David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; 10.1093/nar/gkab31. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.
Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, Žídek A, Green T, Tunyasuvunakool K, Petersen S, Jumper J, Clancy E, Green R, Vora A, Lutfi M, Figurnov M, Cowie A, Hobbs N, Kohli P, Kleywegt G, Birney E, Hassabis D, Velankar S.
Nucleic acids research (2021)
DOI: 10.1093/nar/gkab1061

PDBe-KB: collaboratively defining the biological context of structural data.
PDBe-KB consortium .
Nucleic acids research (2021)
DOI: 10.1093/nar/gkab988

PDBeCIF: an open-source mmCIF/CIF parsing and processing package.
van Ginkel G, Pravda L, Dana JM, Varadi M, Keller P, Anyango S, Velankar S.
BMC bioinformatics Volume 22 (2021) p.383
DOI: 10.1186/s12859-021-04271-9