PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

By P. Hornbeck, J. Kornhauser, S. Tkachev, Bin Zhang, E. Skrzypek, Beth Murray, V. Latham, M. Sullivan. Nucleic Acids Res., 2011

1,608 citations recorded by the source corpus.

PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1 30 000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase–substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase–substrate interactions in PhosphoSitePlus®.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/93e4acf4ba3bca1b379ae8292e73dddb344abd90

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Citations in the corpus

A proteome-scale map of the human interactome network. (2014, background): “Both HI-II-14 and Lit-BM-13 contained significantly more PPIs reflecting known kinasesubstrate relationships (Hornbeck et al., 2012) than the corresponding degree-controlled randomized networks (Figure 2E).”
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations (2014, background): “In any case, throughout this paper, as in our previous 2012 article (8), the terms ‘protein’ and ‘site’ shall apply to a Protein Group and a Site Group, respectively, unless otherwise stated.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “Kinase domains and their target motifs (i.e., specific amino acid sequences in the substrate proteins) can be accessed in resources such as Phosphosite (Hornbeck et al., 2012), NetworKIN and NetPhorest (Linding et al., 2008; Miller et al., 2008).”
Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models (2012, background): “[40] P V Hornbeck, J M Kornhauser, S Tkachev, B Zhang, E Skrzypek, B Murray, V Latham, and M Sullivan.”
Handbook of ion channels (2015, background): “Much of the information listed later can also be found on the PhosphoSitePlus website (41).”
ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016, background): “These modules are regularly modulated by post-translational modifications (PTMs) (10,11) and can be added or removed by alternative transcription or alternative splicing to produce protein isoforms with unique functional properties (12,13).”
A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome (2015, background): “PhosphositePlus [49] provides a network of peptides that can be bound by kinases, yielding in total 6,066 interactions between 1,843 kinases and substrates.”
Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. (2014, methodology): “Comparison of our data to already known phosphorylation events (Hornbeck et al., 2012) suggests that coverage of Tyr phosphorylation is very comprehensive already.”
The ConsensusPathDB interaction database: 2013 update (2012, neutral): “…(protein–protein interactions) (14), PhosphoPOINT (protein–protein and biochemical interactions) (15), PhosphoSitePlus (biochemical interactions) (16), PINdb (protein–protein interactions) (17), SignaLink (biochemical pathways) (18), SMPDB (biochemical pathways) (19), TTD (drug–target…”
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs (2014, background): “ELM (36), PhosphoSitePlus (37) and PhosphoGRID (38), we totally obtained 1016 non-redundant phosphorylation sites in 80 known SUMO-interacting proteins.”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “…genes [Piiril¨a et al., 2006; Samarghitean et al., 2007; Ortutay and Vihinen, 2009], MMR genes [Thompson et al., 2014], protein kinase domain [Sten-berg et al., 2000; Ortutay et al., 2005; Vazquez et al., 2016], phosphorylation sites [Safaei et al., 2011; Hornbeck et al., 2012], and many others.”
D2P2: database of disordered protein predictions (2012, background): “Additionally, the inclusion of PhosphoSitePlus curated PTM annotation lets us see that the disordered inserts between BIN1 isoforms also undergo posttranslational modifications as part of the regulatory process.”