PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update Export

@article{citeulike:6055162, 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. 10.1093/nar/gkp810}, author = {Durek, Pawel and Schmidt, Robert and Heazlewood, Joshua L. and Jones, Alexandra and MacLean, Daniel and Nagel, Axel and Kersten, Birgit and Schulze, Waltraud X.}, citeulike-article-id = {6055162}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp810}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/gkp810v1/.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/gkp810v1/.full.pdf}, day = {30}, doi = {10.1093/nar/gkp810}, journal = {Nucl. Acids Res.}, keywords = {arabidopsis, database, phosphorylation, plant}, month = {October}, pages = {gkp810+}, posted-at = {2009-11-02 04:18:46}, priority = {2}, title = {PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update}, url = {http://dx.doi.org/10.1093/nar/gkp810}, year = {2009} }

TY - JOUR ID - citeulike:6055162 L3 - citeulike-article-id:6055162 N2 - 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. 10.1093/nar/gkp810 JF - Nucl. Acids Res. TI - PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update SP - gkp810 KW - arabidopsis KW - database KW - phosphorylation KW - plant AU - Durek, Pawel AU - Schmidt, Robert AU - Heazlewood, Joshua AU - Jones, Alexandra AU - MacLean, Daniel AU - Nagel, Axel AU - Kersten, Birgit AU - Schulze, Waltraud PY - 2009/10/30/ UR - http://dx.doi.org/10.1093/nar/gkp810 ER -