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.

Aquaria: simplifying discovery and insight from protein structures

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Aquaria page for human tumor suppressor protein p53.

References

  1. 1

    Berman, H.M. et al. Nucleic Acids Res. 28, 235–242 (2000).

    CAS  Article  Google Scholar 

  2. 2

    O'Donoghue, S.I. et al. Nat. Methods 7, S42–S55 (2010).

    CAS  Article  Google Scholar 

  3. 3

    Hartshorn, M.J. J. Comput. Aided Mol. Des. 16, 871–881 (2002).

    CAS  Article  Google Scholar 

  4. 4

    Pettersen, E.F. et al. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  Article  Google Scholar 

  5. 5

    The UniProt Consortium. Nucleic Acids Res. 42, D191–D198 (2014).

  6. 6

    Hunter, S. et al. Nucleic Acids Res. 40, D306–D312 (2012).

    CAS  Article  Google Scholar 

  7. 7

    O'Donoghue, S.I., Meyer, J.E.W., Schafferhans, A. & Fries, K. Bioinformatics 20, 2476–2478 (2004).

    CAS  Article  Google Scholar 

  8. 8

    Sabir, K., Stolte, C., Tabor, B. & O'Donoghue, S.I. Proc. IEEE Symp. Biol. Data Vis. 3, 49–56 (2013).

    Google Scholar 

Download references

Acknowledgements

We thank C. Hammang and V.P. Satagopam for helpful discussions. This work was supported by CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform, as well as the Alexander von Humboldt Foundation. We gratefully acknowledge the support of Amazon AWS in hosting the Aquaria server and in making PSSH2 available as a public data set.

Author information

Affiliations

Authors

Contributions

S.I.O. and A.S. jointly conceived of the project. S.I.O. oversaw the project and wrote the manuscript with contributions from A.S. and K.S.S. Software implementation was led by K.S.S. with contributions from S.I.O., C.S., V.H., N.P., F.A.B. and J.H. Interface design was led by C.S. with contributions from S.I.O. The development of PSSH2, the database underlying Aquaria, was led by A.S. with contributions from M.K., B.W., M.R. and B.R.

Corresponding author

Correspondence to Seán I O'Donoghue.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary texts and figures

Supplementary Figures 1–3 and Supplementary Methods (PDF 603 kb)

Supplementary Video 1

An introduction to using Aquaria (MP4 47683 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

O'Donoghue, S., Sabir, K., Kalemanov, M. et al. Aquaria: simplifying discovery and insight from protein structures. Nat Methods 12, 98–99 (2015). https://doi.org/10.1038/nmeth.3258

Download citation

Further reading

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