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TopFIND, a knowledgebase linking protein termini with function

Nature Methods volume 8, pages 703–704 (2011)Cite this article

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We present 'termini-oriented protein function inferred database' (TopFIND; http://clipserve.clip.ubc.ca/topfind/), a knowledgebase providing integrated information on translated protein N and C termini, their formation by proteolytic processing and their amino acid modifications. TopFIND is open to data contribution from users.

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Figure 1: TopFIND knowledgebase content, terminal acetylation and protein stability.

Change history

  • 12 August 2011

    In the version of this article initially published online, the Figure 1c legend and associated text describing Figure 1c was incorrect. The panels in this figure show N-terminal amino acid occurrence after methonine removal, not all co- and post-translationally processed chains. The error has been corrected for the print, PDF and HTML versions of this article.

References

  1. Doucet, A. et al. Mol. Cell. Proteomics 7, 1925–1951 (2008).

    Article  CAS  Google Scholar 

  2. Impens, F. et al. Proteomics 10, 1284–1296 (2010).

    Article  CAS  Google Scholar 

  3. Schilling, O. et al. Nat. Methods 7, 508–511 (2010).

    Article  CAS  Google Scholar 

  4. Van Damme, P. et al. Nat. Methods 7, 512–515 (2010).

    Article  CAS  Google Scholar 

  5. Rawlings, N.D., Barrett, A.J. & Bateman, A. Nucleic Acids Res. 38, D227–D233 (2010).

    CAS  Google Scholar 

  6. Hwang, C.-S., Shemorry, A. & Varshavsky, A. Science 327, 973–977 (2010).

    Article  CAS  Google Scholar 

  7. Kleifeld, O. et al. Nat. Biotechnol. 28, 281–288 (2010).

    Article  CAS  Google Scholar 

  8. Jawhar, S. et al. J. Biol. Chem. 286, 4454–4460 (2010).

    Article  Google Scholar 

Download references

Acknowledgements

We thank P.F. Huesgen for fruitful discussions. P.F.L. is supported through a Feodor Lynen Research Fellowship of the Alexander von Humboldt Foundation and the German Federal Ministry of Education and Research, and a Michael Smith Foundation for Health Research/Breast Cancer Society of Canada Research Trainee Award. C.M.O. is supported by a Canada Research Chair in Metalloproteinase Proteomics and Systems Biology. This work was supported by a grant from the Canadian Institutes of Health Research and from a program project grant in Breast Cancer Metastases from the Canadian Breast Cancer Research Alliance with funds from the Canadian Breast Cancer Foundation and the Cancer Research Society and with an Infrastructure Grant from the Michael Smith Foundation for Health Research.

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Authors and Affiliations

  1. Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada

    Philipp F Lange & Christopher M Overall

  2. Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada

    Philipp F Lange & Christopher M Overall

  3. Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada

    Philipp F Lange & Christopher M Overall

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  1. Philipp F Lange
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  2. Christopher M Overall
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Correspondence to Christopher M Overall.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Table 1, Supplementary Discussion, Supplementary Methods (PDF 3151 kb)

Supplementary Table 2

Termini inferred from protease cleavage. (XLSX 462 kb)

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Lange, P., Overall, C. TopFIND, a knowledgebase linking protein termini with function. Nat Methods 8, 703–704 (2011). https://doi.org/10.1038/nmeth.1669

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