Phospho.ELM: a database of phosphorylation sites—update 2008

By Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson. Nucleic Acids Res., 2007

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Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING. A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides. Phospho.ELM is available on line at: http://phospho.elm.eu.org

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/794c048acd3d2d35e3248161729fcf142b4966c6

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Citations in the corpus

ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016, background): “These modules are regularly modulated by posttranslational 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).”
Network-based approach to prediction and population-based validation of in silico drug repurposing (2018, background): “ELM58; (3) carefully literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), and from literature-derived lowthroughput experiments from BioGRID59, PINA60, HPRD53, MINT61, IntAct62, and InnateDB63; (4) high-quality PPIs from three-dimensional (3D) protein st”
ELM—the database of eukaryotic linear motifs (2011, background): “ELM resource (25) have been added to the graphical output (Figure 2, top row).”
Prediction of protein disorder based on IUPred (2018, methodology): “Such filtering was also found useful in the interpretation of phosphorylation data extracted from the scientific literature and phosphoproteomic analyses.(61) Various other motif-centric tools, such SLiMPrints or SLiMSearch, also rely on IUPred.”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, methodology): “The core structure of the database has been retained (24,25) and extended, while new features have been implemented to improve data retrieval and presentation.”
Linear Motif Atlas for Phosphorylation-Dependent Signaling (2008, methodology): “ELM ( 26 ), we also obtained a set of 238 phospho-tyrosine sites known to bind 45 different SH2 and PTB domains.”
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs (2014, background): “ELM (36), Phospho-SitePlus (37) and PhosphoGRID (38), we totally obtained 1016 non-redundant phosphorylation sites in 80 known SUMO-interacting proteins.”
NetworKIN: a resource for exploring cellular phosphorylation networks (2007, background): “Decades of targeted studies and recent progress in phosphoproteomics has resulted in a large body of protein phosphorylation data (2).”