Aquaria: simplifying discovery and insight from protein structures - Nature Methods
- ️Schafferhans, Andrea
- ️Thu Jan 29 2015
- Correspondence
- Published: 29 January 2015
- Kenneth S Sabir2,4,
- Maria Kalemanov5,
- Christian Stolte ORCID: orcid.org/0000-0002-8228-41951,
- Benjamin Wellmann5,
- Vivian Ho2,
- Manfred Roos5,
- Nelson Perdigão6,7,
- Fabian A Buske2,8,
- Julian Heinrich1,
- Burkhard Rost5 &
- …
- Andrea Schafferhans ORCID: orcid.org/0000-0002-5569-61865
Nature Methods volume 12, pages 98–99 (2015)Cite this article
-
5060 Accesses
-
94 Altmetric
Subjects
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.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
The features of polyglutamine regions depend on their evolutionary stability
- Pablo Mier
- & Miguel A. Andrade-Navarro
BMC Evolutionary Biology Open Access 24 May 2020
-
BioVR: a platform for virtual reality assisted biological data integration and visualization
- Jimmy F. Zhang
- , Alex R. Paciorkowski
- … Feng Cui
BMC Bioinformatics Open Access 15 February 2019
-
The Dark Proteome Database
- Nelson Perdigão
- , Agostinho C. Rosa
- & Seán I. O’Donoghue
BioData Mining Open Access 20 July 2017
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Additional access options:

References
Berman, H.M. et al. Nucleic Acids Res. 28, 235–242 (2000).
O'Donoghue, S.I. et al. Nat. Methods 7, S42–S55 (2010).
Hartshorn, M.J. J. Comput. Aided Mol. Des. 16, 871–881 (2002).
Pettersen, E.F. et al. J. Comput. Chem. 25, 1605–1612 (2004).
The UniProt Consortium. Nucleic Acids Res. 42, D191–D198 (2014).
Hunter, S. et al. Nucleic Acids Res. 40, D306–D312 (2012).
O'Donoghue, S.I., Meyer, J.E.W., Schafferhans, A. & Fries, K. Bioinformatics 20, 2476–2478 (2004).
Sabir, K., Stolte, C., Tabor, B. & O'Donoghue, S.I. Proc. IEEE Symp. Biol. Data Vis. 3, 49–56 (2013).
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
Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia
Seán I O'Donoghue, Christian Stolte & Julian Heinrich
Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
Seán I O'Donoghue, Kenneth S Sabir, Vivian Ho & Fabian A Buske
School of Molecular Bioscience, The University of Sydney, Sydney, Australia
Seán I O'Donoghue
School of Information Technologies, The University of Sydney, Sydney, Australia
Kenneth S Sabir
Department for Bioinformatics and Computational Biology, Technische Universität München, Munich, Germany
Maria Kalemanov, Benjamin Wellmann, Manfred Roos, Burkhard Rost & Andrea Schafferhans
Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
Nelson Perdigão
Instituto de Sistemas e Robótica, Lisboa, Lisbon, Portugal
Nelson Perdigão
St. Vincent's Clinical School, The University of New South Wales (UNSW), Sydney, Australia
Fabian A Buske
Authors
- Seán I O'Donoghue
You can also search for this author in PubMed Google Scholar
- Kenneth S Sabir
You can also search for this author in PubMed Google Scholar
- Maria Kalemanov
You can also search for this author in PubMed Google Scholar
- Christian Stolte
You can also search for this author in PubMed Google Scholar
- Benjamin Wellmann
You can also search for this author in PubMed Google Scholar
- Vivian Ho
You can also search for this author in PubMed Google Scholar
- Manfred Roos
You can also search for this author in PubMed Google Scholar
- Nelson Perdigão
You can also search for this author in PubMed Google Scholar
- Fabian A Buske
You can also search for this author in PubMed Google Scholar
- Julian Heinrich
You can also search for this author in PubMed Google Scholar
- Burkhard Rost
You can also search for this author in PubMed Google Scholar
- Andrea Schafferhans
You can also search for this author in PubMed Google Scholar
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
Rights and permissions
About this article
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
Published: 29 January 2015
Issue Date: February 2015
DOI: https://doi.org/10.1038/nmeth.3258