title: PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update.
abstract: 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.
authors.affiliation: Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
authors.forename: Pawel
authors.initials: P
authors.lastname: Durek
authors.forename: Robert
authors.initials: R
authors.lastname: Schmidt
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Heazlewood
authors.forename: Alexandra
authors.initials: A
authors.lastname: Jones
authors.forename: Daniel
authors.initials: D
authors.lastname: MacLean
authors.forename: Axel
authors.initials: A
authors.lastname: Nagel
authors.forename: Birgit
authors.initials: B
authors.lastname: Kersten
authors.forename: Waltraud X
authors.initials: WX
authors.lastname: Schulze
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030562:Databases, Protein; D017343:Genes, Plant; D018745:Genome, Plant; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D012984:Software
chemical_list: D029681:Arabidopsis Proteins; D010750:Phosphoproteins