Post-Translational Modification site Prediction - User Interface (PTMP-UI):

    Since the diversity in the user interface (UI) of different prediction servers could greatly hinder experimental biologists in using these servers, we proposed a protocol of a unified user interface (UI) for in silico prediction servers for prediction of post-translational modification sites, based on our own work and other work on PTM site prediction. Computational biologists may follow this protocol to provide a uniform user interface, regardless of the PTM types and the computation algorithms. And wet lab biologists would be able to use any PTM site prediction servers compliant to this protocol after getting familiar with one of them.    

  • For PTMs analyses and predictions, we collected most of related online databases, web services, and tools at LINK page.


    Rationale for a unified UI:
    1. Input: one or multiple protein primary sequences in FASTA format
    2. Output: predicted PTM sites position and modified residue type
    3. Output: flanking peptide of the PTM site
    4. Output: evaluation score or probability of the predicted PTM site
    5. "Example-then-Submit": make a "Example" button to load example data and click on "Submit" button for demo prediction

    For references and publication of results, please cite the following articles:

     A general user interface for prediction servers of proteins' post-translational modification sites
     Fengfeng Zhou, Yu Xue, Xuebiao Yao and Ying Xu
     Nature Protocols.2006; 7: 1318-1321

     [Abstract] [Full Text]


     GPS: A computational protocol for kinase-specific phosphorylation site prediction
     Yu Xue, Fengfeng Zhou, Ying Xu and Xuebiao Yao
     Nature Protocols.2007; DOI: 10.1038/nprot.2007.219

     [Full Text]


    ☆ Contact:

    Prof. & Dr. Yu Xue (Personal CV)

    Ph.D., Professor,
    Principle Investigator,
    Department of Biomedical Engineering,
    College of Life Science and Technology,
    Huazhong University of Science and Technology,
    No. 1037, Luoyu Road,
    Wuhan, 430074, Hubei, P.R.China

    Phone: +86-27-87793903
    Fax: +86-27-87793172
    Personal Website:
    ResearcherID Google Scholar Sciencenet's Blog


    Last updated: Jan. 13th, 2013
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