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. 2004 Jun 22:5:79.
doi: 10.1186/1471-2105-5-79.

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

Francesca Diella  1 , Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Kuster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J Gibson
Affiliations

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

Francesca Diella et al. BMC Bioinformatics. .

Abstract

Background: Post-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.

Description: Phospho.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.

Conclusion: Phospho.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.

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Figures

Figure 1
Figure 1
The simplified Phospho.ELM database scheme. The key data objects are Substrates (phosphoprotein) and Instances for which relevant information is stored, as well as links to external databases. pkey and fkey stand for "primary key" and "foreign key", respectively.
Figure 2
Figure 2
A) Scheme for the PI3Kp85 protein with domains and phosphorylation sites. B) Output example of keyword search using PI3Kp85. Information about the phosphorylated sites includes the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation and links to additional information for the substrate and other relevant databases.
See this image and copyright information in PMC

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