PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

By P. Durek, Robert Schmidt, J. Heazlewood, Alexandra Jones, D. MacLean, Axel Nagel, B. Kersten, Waltraud X. Schulze. Nucleic Acids Res., 2009

388 citations recorded by the source corpus.

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows ‘on-the-fly’ prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.

Subfields: Molecular Biology, Plant Science, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b1892e7f9f09dd786e4a1b9ee1f6edaf14520227

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Citations in the corpus

The JAZ Proteins: A Crucial Interface in the Jasmonate Signaling Cascade (2011, background): “Nonetheless, a tobacco homolog of JAZ3, NbPPS3, has been identified as a kinase target (Katou et al., 2005) and, at least for JAZ12 (At5g20900), phosphopeptides have been detected (PhosPhAt 3.0) (Durek et al., 2010), suggesting that JAZ function is regulated by phosphorylation.”
Biological sequence motif discovery using motif-x. (2011, methodology): “This data format is also becoming increasingly adopted by protein posttranslational modification databases (Hornbeck et al., 2004; Durek et al., 2010; Dinkel et al., 2011), as well as in the supplemental data of large-scale PTM studies (Matic et al., 2010; Rigbolt et al., 2011).”