Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

A general user interface for prediction servers of proteins' post-translational modification sites

Nature Protocols volume 1, pages 1318–1321 (2006)Cite this article

Abstract

Post-translational modifications (PTMs) of proteins play essential roles in governing the functions and dynamics of proteins and are implicated in many cellular processes. Several types of PTMs have been investigated through computational approaches, including phosphorylation, sumoylation, palmitoylation, and lysine and arginine methylation, among others. Because the large diversity in the user interfaces (UIs) of different prediction servers for PTMs could possibly hinder experimental biologists in using these servers, we propose to develop a protocol for a unified UI for PTM prediction servers, based on our own work and that of other groups on PTM site prediction. By following this protocol, tool developers can provide a uniform UI regardless of the PTM types and the underlying computational algorithms. With such uniformity in the UI, experimental biologists would be able to use any PTM prediction server compliant with this protocol once they had learned to use one of them. It takes a typical PTM prediction server compliant with this unified UI several minutes to calculate the prediction results for a protein 1,000 amino acids in length.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2
Figure 3

Similar content being viewed by others

References

  1. Zhou, F., Xue, Y., Chen, G. & Yao, X. GPS: a novel group-based phosphorylation prediction and scoring method. Biochem. Biophys. Res. Commun. 325, 1443–1448 (2004).

    Article  CAS  Google Scholar 

  2. Xue, Y., Zhou, F., Zhu, M., Ahmed, K., Chen, G. & Yao, X. GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res. 33, W184–W187 (2005).

    Article  CAS  Google Scholar 

  3. Obenauer, J.C., Cantley, L.C. & Yaffe, M.B. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31, 3635–3641 (2003).

    Article  CAS  Google Scholar 

  4. Xue, Y., Li, A., Wang, L., Feng, H. & Yao, X. PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 7, 163 (2006).

    Article  Google Scholar 

  5. Blom, N., Sicheritz-Ponten, T., Gupta, R., Gammeltoft, S. & Brunak, S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4, 1633–1649 (2004).

    Article  CAS  Google Scholar 

  6. Kim, J.H., Lee, J., Oh, B., Kimm, K. & Koh, I. Prediction of phosphorylation sites using SVMs. Bioinformatics 20, 3179–3184 (2004).

    Article  CAS  Google Scholar 

  7. Iakoucheva, L.M. et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32, 1037–1049 (2004).

    Article  CAS  Google Scholar 

  8. Xue, Y., Zhou, F., Fu, C., Xu, Y. & Yao, X. SUMOsp: a web server for SUMOylation site prediction. Nucleic Acids Res. 34, W254–W257 (2006).

    Article  CAS  Google Scholar 

  9. Zhou, F., Xue, Y., Yao, X. & Xu, Y. CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinformatics 22, 894–896 (2006).

    Article  CAS  Google Scholar 

  10. Chen, H., Xue, Y., Huang, N., Yao, X. & Sun, Z. MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res. 34, W249–W253 (2006).

    Article  CAS  Google Scholar 

  11. Sayle, R.A. & Milner-White, E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374–376 (1995).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

F. Zhou's and Y. Xu's work is supported in part by the National Science Foundation (NSF/DBI-0354771, NSF/ITR-IIS-0407204, NSF/DBI-0542119, NSF/CCF0621700) and a Distinguished Scholar award from the Georgia Cancer Coalition. Y. Xue's and X. Yao's work is supported by Chinese Natural Science Foundation (39925018, 30270654 and 30270293), Chinese Academy of Science (KSCX2-2-01), Chinese 973 project (2002CB713700), Chinese Minister of Education (20020358051), American Cancer Society (RPG-99-173-01), National Institutes of Health (DK56292; CA92080) and a Distinguished Scholar award from the Georgia Cancer Coalition.

Author information

Author notes

  1. Fengfeng Zhou and Yu Xue: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemical and Molecular Biology, Computational Systems Biology Laboratory, and Institute of Bioinformatics, University of Georgia, Athens, 30602, Georgia, USA

    Fengfeng Zhou & Ying Xu

  2. Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of China, Hefei, 230027, China

    Yu Xue & Xuebiao Yao

  3. Department of Physiology and Cancer Research Program, Morehouse School of Medicine, Atlanta, 30310, Georgia, USA

    Xuebiao Yao

Authors
  1. Fengfeng Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xuebiao Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ying Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Xuebiao Yao or Ying Xu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhou, F., Xue, Y., Yao, X. et al. A general user interface for prediction servers of proteins' post-translational modification sites. Nat Protoc 1, 1318–1321 (2006). https://doi.org/10.1038/nprot.2006.209

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2006.209

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing