Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins

By Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj S. Blom, Toby J. Gibson. BMC Bioinformatics, 2004

440 citations recorded by the source corpus.

BackgroundPost-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DescriptionPhospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.ConclusionPhospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.

Subfields: Biophysics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/edc66001123825851acc62eff76d23a1f38886bb

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Citations in the corpus

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites (2007, background): “ELM [26] are already comprehensive databases that contain phosphorylation sites from different projects.”
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database (2011, methodology): “In Step (5), we manually check the list of PTMs from the controlled vocabulary that contained either zero experimental or zero non-experimental hits from the Swiss-Prot database to ensure that these particular PTMs were not present in the database.”
GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S (2008, methodology): “ELM data-base (21).”
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (2006, methodology): “ELM database (Diella et al., 2004) and the Human Proteome Reference Database (Peri et al., 2004) and have uploaded previous phosphoproteome data sets to Phosida.”
Systematic discovery of in vivo phosphorylation networks. (2007, background): “ELM (in total 7207 sites on 2540 proteins, including large-scale mass spectrometry data [Diella et al., 2004]).”
Using graph theory to analyze biological networks (2011, neutral): “ELM [31], NetPhorest [32] or PHOSIDA [33].”
Discovering Sequence Motifs with Arbitrary Insertions and Deletions (2008, methodology): “ELM database [43], and grouped by kinase family.”
Phospho.ELM: a database of phosphorylation sites—update 2008 (2007, neutral): “(13).”
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes (2006, methodology): “Although several methods have been described in the literature, only a limited number of them are available to the public ( 19 ,39).”