A powerful web resource for viewing proteins

Scientists have announced the release of Aquaria - a publicly available web resource that streamlines and simplifies the process of gleaning insight from 3D protein structures.

The project, which began in 2009, has involved an international team of around a dozen programmers and bioinformatics experts. It was led by Dr Seán O’Donoghue, from The Garvan Institute of Medical Research and CSIRO, in collaboration with Dr Andrea Schafferhans from the Technical University of Munich.

Aquaria is built on the Protein Data Bank, which contains just over 100,000 protein structures. Dr O’Donoghue explained that the data bank is “a fantastic resource containing a wealth of detail about the molecular processes of life, but we were aware that few biologists take full advantage of it”. The team created Aquaria to make this information more accessible and easy to use.

“What we’ve done is to layer in a lot of extra useful information,” Dr O’Donoghue said. “For example, we’ve added protein sequences that do not yet have a structure - but are similar to something in the Protein Data Bank. That meant we first had to find all these similarities.”

Over 500,000 protein sequences without known structures were compared with the 100,000 known protein structures. This resulted in around 46 million computer models, which are now available in Aquaria.

“Aquaria is fast, it comes with an easy-to-use interface and contains twice as many models as all other similar resources combined,” said Dr O’Donoghue. All a scientist needs to do is enter the name of their favourite protein.

Aquaria’s flexibility and extensibility allows information to be combined quickly and easily. For example, said Dr O’Donoghue, users can view genetic differences between individuals mapped onto 3D structures.

“You can add single nucleotide polymorphisms (SNPs) that cause protein changes, then visualise exactly where those changes occur in the protein structure,” he said. “This provides valuable insight into why proteins sometimes completely change their function as a result of one small change in the DNA code.

“You can then ask interesting questions like ‘Does this set of SNPs cluster in 3D?’ and the answers to such questions can set new research directions.”

Aquaria is available at http://aquaria.ws and will be useful for a broad range of life scientists, from medical researchers to scientists studying agriculture, biosecurity, ecology and nutrition. Interested parties can read about the tool in Nature Methods or take part in a special webinar scheduled for 3 February at 9 am AEDT.

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