PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update.
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update.
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DOI：
10.1093/nar/gkp810
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发表时间：
2010-01
影响因子：
14.9
通讯作者：
Schulze WX
中科院分区：
文献类型：
--
作者：
Durek P;Schmidt R;Heazlewood JL;Jones A;MacLean D;Nagel A;Kersten B;Schulze WX
拟南芥磷酸化位点的PhosPhAt数据库最初于2007年8月启动。从那时起，随着数据库条目增加了10倍，PhosPhAt （PhosPhAt .mpimp-golm.mpg.de）的功能得到了相当大的升级和重新设计。PhosPhAt现在更像是一个包含高级搜索功能的web应用程序，允许通过布尔项进行组合搜索。结果输出现在包括注释碎片光谱的交互式可视化，以及将光谱和肽序列导出为文本文件以供其他应用程序使用的能力。我们还实现了与其他网络资源的动态链接，从而增加了与外部蛋白质相关数据的磷酸酶特异性信息。对于具有响应外部刺激的动态行为信息的实验性磷酸化位点，我们显示了简单的时间分辨图。我们已经包括pT和pY站点的预测和更新的pS预测。访问预测算法现在允许“实时”预测任何用户上传的蛋白质序列的磷酸化。蛋白质Pfam结构域结构现在被映射到蛋白质序列显示旁边的实验和预测磷酸化位点。最后，利用MAPMAN本体实现了蛋白质的功能标注。这些新进展使PhosPhAt资源成为植物科学以外的整个科学界的有用和强大的工具。
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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影响因子：
14.9
作者：
Heazlewood, Joshua L.;Verboom, Robert E.;Millar, A. Harvey
通讯作者：
Millar, A. Harvey
影响因子：
7.2
作者：
Nuhse, Thomas S;Bottrill, Andrew R;Jones, Alexandra M E;Peck, Scott C
通讯作者：
Peck, Scott C
影响因子：
14.9
作者：
Riaño-Pachón DM;Nagel A;Neigenfind J;Wagner R;Basekow R;Weber E;Mueller-Roeber B;Diehl S;Kersten B
通讯作者：
Kersten B
影响因子：
10.5
作者：
Popescu, Sorina C.;Popescu, George V.;Dinesh-Kumar, Savithramma P.
通讯作者：
Dinesh-Kumar, Savithramma P.
影响因子：
7.4
作者：
Reiland, Sonja;Messerli, Gaelle;Baginsky, Sacha
通讯作者：
Baginsky, Sacha