Tool:Aquaria: simplifying discovery and insight from protein structures

Question

[Aquaria team]

Dear community,

People interested in using 3D structures might like Aquaria, a new, free and open-source web resource for biologists that simplifies the process of gaining insight from protein structures (O'Donoghue et al., Nature Methods, 2015). For all SwissProt protein sequences, Aquaria provides a concise visual summary of all related 3D structures, and the facility to map features onto related structures (e.g., SNPs, PTMs, domains, etc.), including user-defined features (see API docs).

On Firefox and Safari it uses the SRS3D Viewer, an intuitive Java Applet that allows control of the molecular graphics via familiar mouse and keyboard commands, e.g., holding shift while clicking select a range of residues. It also supports control using the Leap Motion camera. On Chrome it uses PV, a JavaScript molecular graphics tool based on WebGL - PV currently has much less functionality, however it is being rapidly developed.

Probably the best way to get started is to watch the 6 min. introductory video, and the more detailed 46 min. Aquaria launch event.

The Aquaria team (including Sean O'Donoghue, Kenny Sabir, Christian Stolte, Andrea Schafferhans)

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FAQ

There are some PDB files that I cannot find in Aquaria - why is that?

There may be several reasons: (1) If a PDB entry is relatively new, it may be missing from the sequence-to-structure alignment database that underlies Aquaria (called PSSH2). If the PDB entry is older than three months, please post the BioStars forum. (2) Currently, Aquaria does not include PDB structures that exceed the size of the traditional PDB file format limits (>62 chains or >99,999 atoms).

Why can't I see the amino acid sequence under the 3D structure?

You are probably using Chrome - notice the red 'Alert' message at the top of windows that warns of limited functionality on Chrome. The 3D viewer used on Chrome is a JavaScript/WebGL alternative still being developed. To access the full-featured viewer (a Java applet), you need to use Firefox or Safari.

Can I see a multiple sequence alignment view of the information in the Matching Structures section?

Aquaria is not designed to enable detailed viewing and editing of MSAs. However, using the Aquaria API you can fetch information on the alignments shown in the 'Matching Structures' section. You could then reformat and display that information in a program designed to show and edit MSA details, e.g., Jalview.

Answer 1

[Mary]

Hi folks--love the idea of support for your software here at Biostars. I've been exploring Aquaria a bit, and I have a question for you about how to change the visualization. It may be in the documentation but I haven't quite figured it out yet.

I am looking at proteins with many subunits, like these hemolysins: http://aquaria.ws/P09616/7ahl/A

When it loads, I can see an individual subunit--which is effective and I get it. The other subunits are shadowed though. How do I make the rest of them fill out with full color?

[Aquaria team]

Hi Mary,

you can see all subunits in their full glory by turning off "Autofocus" (click the checkmark in the menu bar, top right).

Thanks for pointing this out - I have to add that to the documentation!

Cheers,
Christian

Christian Stolte
Senior Bioinformatics Specialist
CSIRO Digital Productivity
http://www.csiro.au

Answer 2

[Aquaria team]

An even quicker solution is to double click anywhere on the background in the 3D view. This effectively zooms out to show all chains equally - if you then click on any part of any chain, the view will zoom to show this chain, partly hiding the others via semi-transparency. This ability to focus on one chain at a time is what we call 'AutoFous' - it can be disabled, as Christian suggests.