Being able to visualize the three-dimensional structure of proteins has been of great interest to scientists since long before the genomic age. Now, a new web resource open to the public is trying to simplify the process of generating 3D protein structures.

The project, titled Aquaria, was led by Sean O’Donoghue, Ph.D., from The Garvan Institute of Medical Research and Commonwealth Scientific and Industrial Research Organization (CSIRO), in collaboration with Andrea Schafferhans, Ph.D., from the Technical University of Munich. This technical undertaking began in 2009 and has incorporated a team of over a dozen computer programmers and bioinformatic scientists from around the world.

This adaptaive new resource for life scientists was announced today in Nature Methods in an article entitled “Aquaria: simplifying discovery and insight from protein structures”.

Aquaria was built atop the long running Protein Data Bank (PDB), a repository for 3D structures of biomolecules, originally established in 1971 at Brookhaven National Laboratory that contains in excess of 100,000 protein structures.

“The Protein 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,” stated Dr. O'Donoghue. “So we created Aquaria to make this valuable information more accessible and easier to use for discovery purposes.”

The Aquaria team took more than 500,000 protein sequences and compared them with the known protein structures from PDB, which yielded around 46 million computer models. That equates to at least one matching structure for 87% of sequences on the Swiss-Prot database and a median of 35 structures per protein.

“Aquaria is fast, it comes with an easy-to-use interface and contains twice as many models as all other similar resources combined. It also allows users to view additional information — such as genetic differences between individuals — mapped onto 3D structures,” explained Dr. O'Donoghue.

Researchers will be able to ask interesting questions about protein structures. For instance, investigators can add in known or hypothesized single nucleotide polymorphisms (SNP’s) and then have the ability to precisely visualize where the changes occur within the protein structure. 

“Aquaria is designed for biologists; its user interface creates clear and useful default views that show only the most relevant structural information tightly integrated with sequence, features and text that provide biological context,” the paper concluded.

Previous articleAstraZeneca and MD Anderson Join to Improve Outcomes for Gynecologic Cancer Patients
Next articleMany Small Gene Jumps in Mammals, One Giant Evolutionary Leap to Pregnancy