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  PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A., MacLean, D., Nagel, A., et al. (2010). PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Research, 38(Database issue), D828-D834. doi:10.1093/nar/gkp810.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2426-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-1AE2-8
Genre: Journal Article

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 Creators:
Durek, P.1, Author              
Schmidt, R.2, Author              
Heazlewood, J. L.3, Author
Jones, A.3, Author
MacLean, D.3, Author
Nagel, A.1, 4, Author              
Kersten, B.1, Author              
Schulze, W. X.5, Author              
Affiliations:
1BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
2Genome Structure and Function, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753308              
3External Organizations, ou_persistent22              
4Integrative Carbon Biology, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753329              
5Signalling Proteomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753330              

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Free keywords: plasma-membrane proteins phosphoproteomic analysis data sets in-vivo networks identification mechanism responses reveals
 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.

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Language(s): eng - English
 Dates: 2009-10-302010
 Publication Status: Published in print
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 Table of Contents: -
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 Identifiers: ISI: ISI:000276399100129
DOI: 10.1093/nar/gkp810
ISSN: 1362-4962 (Electronic)0305-1048 (Linking)
URI: ://000276399100129http://nar.oxfordjournals.org/content/38/suppl_1/D828.full.pdf
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Title: Nucleic Acids Research
  Other : Nucleic Acids Res.
Source Genre: Journal
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Publ. Info: -
Pages: - Volume / Issue: 38 (Database issue) Sequence Number: - Start / End Page: D828 - D834 Identifier: ISSN: 0301-5610
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000262810