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Aquaria: simplifying discovery and insight from protein structures

Nature Methods volume 12, pages 98–99 (2015)Cite this article

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To the Editor:

Since the discovery of the DNA double helix, biologists have been aware that atomic-scale three-dimensional (3D) structures can provide significant insight. The Protein Data Bank1 (PDB) contains a wealth of structural information, but few biologists take full advantage of it2. Thus, we developed Aquaria (http://aquaria.ws), a publicly available web resource that streamlines and simplifies the process of gleaning insight from protein structures.

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

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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

Authors and Affiliations

  1. Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia

    Seán I O'Donoghue, Christian Stolte & Julian Heinrich

  2. Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia

    Seán I O'Donoghue, Kenneth S Sabir, Vivian Ho & Fabian A Buske

  3. School of Molecular Bioscience, The University of Sydney, Sydney, Australia

    Seán I O'Donoghue

  4. School of Information Technologies, The University of Sydney, Sydney, Australia

    Kenneth S Sabir

  5. Department for Bioinformatics and Computational Biology, Technische Universität München, Munich, Germany

    Maria Kalemanov, Benjamin Wellmann, Manfred Roos, Burkhard Rost & Andrea Schafferhans

  6. Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal

    Nelson Perdigão

  7. Instituto de Sistemas e Robótica, Lisboa, Lisbon, Portugal

    Nelson Perdigão

  8. St. Vincent's Clinical School, The University of New South Wales (UNSW), Sydney, Australia

    Fabian A Buske

Authors
  1. Seán I O'Donoghue
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  2. Kenneth S Sabir
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  3. Maria Kalemanov
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  4. Christian Stolte
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  5. Benjamin Wellmann
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  6. Vivian Ho
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  7. Manfred Roos
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  8. Nelson Perdigão
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  9. Fabian A Buske
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  10. Julian Heinrich
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  11. Burkhard Rost
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  12. Andrea Schafferhans
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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.

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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)

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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

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