Open Access Highly Accessed Database

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

Francesca Diella13, Scott Cameron2, Christine Gemünd3, Rune Linding3, Allegra Via4, Bernhard Kuster1, Thomas Sicheritz-Pontén5, Nikolaj Blom5 and Toby J Gibson3*

Author Affiliations

1 Cellzome AG, Heidelberg, Germany

2 Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee, UK

3 Structural and Computational Biology Programme, European Molecular Biology Laboratory, 69012 Heidelberg, Germany

4 Center for Molecular Biolinformatics Dept of Biology, Tor Vergata University, Rome, Italy

5 Center for Biological Sequence Analysis-DTU Lyngby, Denmark

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BMC Bioinformatics 2004, 5:79  doi:10.1186/1471-2105-5-79

Published: 22 June 2004

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 webcite 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.

Keywords:
post-transcriptional modification; protein kinase; bioinformatics