Virtual reality and protein structure

The use of virtual reality has transformed the understanding of protein structure and function at the University of Arkansas.

The advanced visualisation company Virtalis has installed an entry-level ActiveMove Virtual Reality (VR) system and its software plug-in that enhances the stereoscopic 3D viewing of PyMOL at the University of Arkansas.

The system allows staff and students at the Centre for Protein Function and Structure within the Department of Chemistry and Biochemistry to be immersed in and interact with the VR environment.

Dr James Hinton, Professor, explained: “Thanks to funding from the National Institute of Health, which has supported our centre for a dozen years, we have superb instrumentation. However, protein structures are very large, making them hard to understand in 2D. Now we can see the intricate three-dimensional geometry of the folded protein structures. Using movies made with this system, we are able to study protein-protein interaction and docking of proteins with small molecules for the examination of binding sites and how changes in the small molecule affects the binding process.

With ActiveMove, data can be visualised in stereoscopic 3D with full immersion and interaction, thanks to Virtalis’s integrated head and hand tracking solution. This added functionality alters the perspective of the visuals according to the user’s position and orientation within the scene. Crucially for Dr Hinton and his team, Virtalis has brought these qualities to PyMOL, a molecular viewer, giving the ability to interact with chemical structures via a tracked, handheld device.

PyMOL renders publication-quality illustrations of macromolecules, including drug targets. Molecular animations can be created through simple object and camera motions or through input of trajectories from molecular dynamics simulations and other dynamic conformational ensembles.

Steve Carpenter, Virtalis’s PyMOL specialist, explained: “Increasing numbers of our customers hail from the biochemistry and life sciences fields. They asked us to create this plug-in to enhance the usability of PyMOL for them. We worked with the product’s late creator, Warren DeLano, to add 3D tracking functionality to the software.”

The team at the University of Arkansas has already broadened the use of its Virtalis system beyond the research arena. It is being routinely used for teaching both graduate and undergraduate students and has even been deployed as a recruiting tool for the department.

“People are rather blasé when I introduce the system,” said Hinton, “but I wait for the inevitable gasps that follow as they see its power. This is usually followed by laughter as they experience something they hadn’t expected.”

Dr Hinton’s search for the missing link that would allow him to visualise in 3D was lengthy. “I knew what I wanted and I knew want I needed,” he commented. “I tried hard to find the solution and the VR enabling of PyMOL by Virtalis makes interacting with protein structures in the ActiveMove very easy. We use the National Protein Databank to obtain the structures and load this data into PyMOL. I already have several people trained to run the ActiveMove, but the system is so easy to use, I will be broadening its use further.”

ActiveMove comprises an active, stereoscopic 3D projector with a rear projection screen in a dedicated enclosure, coupled with a PC, eyewear, head and hand tracking, installation and Virtalis enabling software and support.

Virtalis

www.virtalis.com