蛋白质磷酸化修饰相关计算资源汇总

For publication of results, please cite the following article: A summary of computational resources for protein phosphorylation .Yu Xue , Xinjiao Gao, Cao Jun, Liu Zexian, Changjiang Jin, Longping Wen, Xuebiao Yao, and Jian Ren . Current Protein & Peptide Science. 2010 ; 11(6):485-496

Introduction :

    Protein phosphorylation is the most ubiquitous post-translational modification (PTM), and plays important roles in most of biological processes. Identification of site-specific phosphorylated substrates is fundamental for understanding the molecular mechanisms of phosphorylation. Besides experimental approaches, prediction of potential candidates with computational methods has also attracted great attention for its convenience and fast-speed. In this review, we present a comprehensive but brief summarization of computational resources of protein phosphorylation, including phosphorylation databases, prediction of non-specific or organism-specific phosphorylation sites, prediction of kinase-specific phosphorylation sites or phospho-binding motifs, and other tools. A testing data set prepared from Phospho.ELM 6.0 is available at: Comparison_data .

    We apologized that the computational studies without any web links of databases or tools will not be included in this compendium, since it's not easy for experimentalists to use studies directly. We are grateful for users feedback. Please inform Prof. Yu Xue or Prof. Jian Ren to add, remove or update one or multiple web links below.

Index :

<1> Phosphorylation Databases

<2> Prediction of non-specific or organism-specific phosphorylation sites

<3> Prediction of kinase-specific phosphorylation sites or phospho-binding motifs

<4> Miscellaneous tools

<5> Detection of potential phosphorylation sites from mass spectrometry data

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<1> Phosphorylation Databases :

1. Phospho.ELM 8.3 (PhosphoBase) : contains 5,115 experimentally verified phosphorylated proteins from different species with 2,746 tyrosine, 15,972 serine and 3,283 threonine sites. All instances were manually collected from scientific literature (Diella, et al. , 2004 ; Diella, et al. , 2008 ).

2. PhosphoSitePlus : a new version of PhosphoSite, is a web-based database to collect protein modification sites, including protein phosphorylation sites from scientific literature as well as high-throughput discovery programs. Currently, PhosphoSitePlus contains 78,022 phosphorylation sites (Hornbeck, et al. , 2004 ).

3. PhosphoNET : PhosphoNET presently holds data on more than 74,000 phosphorylation sites in over 12,400 human proteins that have been collected from the scientific literature and other reputable websites. It features direct links to several other useful websites, and will continue to expand as a useful portal for phosphoproteomics information.

4. HPRD release 9 : HPRD currently contains information for 16,972 PTMs which belong to various categories with phosphorylation (10,858), dephosphorylation (3,118) and glycosylation (1,860) forming the majority of the annotated PTMs. At least one enzyme responsible for PTMs has been annotated for 8,960 PTMs, which resulted in the documentation of 7,253 enzyme - substrate relationships (Keshava Prasad, et al ., 2009 ).

5. PHOSIDA (Mirror website ): a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts non-specific phosphosites (Gnad, et al. , 2007 ; Gnad, et al. , 2009 ).

6. PhosphoPep v2.0 : contains MS-derived phosphorylation data from 4 different organisms, including fly (Drosophila melanogaster ), human (Homo sapiens ), worm (Caenorhabditis elegans ), and yeast (Saccharomyces cerevisiae ) (Bodenmiller, et al. , 2008 ).

7.