Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer

To the Editor:

We report the Autodesk Molecule Viewer (www.molviewer.com), an accessible, web-based communication tool for visualizing biomolecular structures.

The first protein crystal structures were solved with the aid of physical models1. Since then, there has been a strong effort among researchers to represent molecules in 3D with virtual models. With the rise of computers in the '60s, it became possible to automatically generate stereoscopic images to visualize molecules on paper in 3D2. By the '80s came the first immersive and interactive virtual 3D models3. Today, there exist several macromolecular visualization programs4, some of which can produce an immersive virtual reality (VR) environment5,6. However, such VR setups are costly, restricted to a single station, and generally not very portable. Thus, they are not feasible for use in most educational or research settings.

We wish to inform readers interested in biomolecular structures about an easy- and free-to-use tool, which enables scientists to prepare, explore, and share interactive 3D and immersive VR structural walkthroughs directly in a web browser (Fig. 1a). This online tool, the Autodesk Molecule Viewer, allows users to easily import atomic coordinates, generate structural representations, annotate in space, and store individual 3D structural snapshots in the cloud for dissemination.

Figure 1: VR using the Autodesk Molecule Viewer.
figure1

(a) Screenshot of the Autodesk Molecule Viewer tool in its editing mode. (b) Exploring structures using a desktop-machine-linked VR headset through a web browser. (c) VR content loaded onto a smartphone web browser for exploration with an inexpensive cardboard VR device. (d) Audience members following a VR-based structural biology seminar.

Some of the major advantages of the Autodesk Molecule Viewer are its intuitive user interface, snapshot, annotation and captioning tools, and architecture to widely distribute and access prepared content. It is browser based (no download or installation is required), and this makes it very accessible. Prepared 3D models as large as entire viruses can be shared through unique URLs (e.g., http://autode.sk/natmethods) and loaded within seconds on computers, tablets, or smartphones. Content generated with this tool can be experienced in VR with headsets simply by accessing a shared URL via a desktop machine (Fig. 1b) or a smartphone web browser (Fig. 1c).

We have delivered structural biology presentations entirely in VR at international scientific conferences to hundreds of audience members (Fig. 1d). Conference attendees followed the presentation with the freedom to inspect highlighted structural features from any angle in an immersive VR environment on their own smartphones using the standard, inexpensive cardboard VR devices that were provided. Interactive components can also be embedded into websites, content may be exhibited at gatherings, and information can be relayed to experts and casual users alike via URLs distributed in person or through email, instant messaging, or social media. As researchers and educators, we believe that accessible communication technology fosters dialog between scientists and brings science to a broader audience.

The Autodesk Molecule Viewer and relevant documentation, including a user guide, can be accessed at www.molviewer.com.

AUTHOR CONTRIBUTIONS

A.R.B. prepared and presented structural biology content in VR at international conferences with guidance from M.W. and O.P.E. All authors participated in discussing, writing and revising of the manuscript.

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Acknowledgements

We acknowledge D. Amago, E. Groban, D. Hylbert, P. Jones, A. Kimoto, F. Mazzoldi, D. Parker, M. Tinnus, A. Virshup and M. Zyracki (Autodesk Life Sciences) for the creation and development of the Autodesk Molecule Viewer. We thank Autodesk for supplying cardboard VR devices at international conferences. We thank the Canadian Institute for Advanced Research and the Canada Excellence Research Chairs program (both to O.P.E.) for financial support to attend and present at international conferences. O.P.E. holds the Anne and Max Tanenbaum Chair in Neuroscience.

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Correspondence to Oliver P Ernst.

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A.R.B. and M.W. are employed by Autodesk. M.W. owns Autodesk stock.

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Balo, A., Wang, M. & Ernst, O. Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer. Nat Methods 14, 1122–1123 (2017). https://doi.org/10.1038/nmeth.4506

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