Virtual Reality uses in Drug Discovery

Tom Goddard
August 7, 2019
For Tom Ferrin's ACS talk August 26


Types of 3D biology data visualized with VR

We are trying VR in ChimeraX for 3D biology data at various scales: atomic models, cryoEM, light microscopy time series, medical imaging.

Opiods bound to opioid receptor, computational docking. Crawling neutrophils, light microscopy.
Translation initiation factor inhibitor, cryoEM. Lung CT scan.

Jacobson lab weekly VR group meeting

Video illustration of VR discussion of drug docking.

What problems benefit from VR?

Example where VR helped understand drug resistance

Receptor tyrosine kinase (KIT) with docked midostaurin and avapritinib drugs. KIT mutations in circles inhibit drug avapritinib (blue) although through an indirect interaction that moves P-loop (green ribbon) which blocks binding.

cryoEM model refinement can benefit from VR

Example: Photosynthesis supercomplex

Chlorophyll and other ligands showing cryoEM density at ~3 Angstrom resolution.
Photosystem II light harvesting supercomplex (ligands in yellow) Ligands with proteins hidden: chlorophyll and fucoxanthin pigment (green), lipids (orange), ion-like (magenta).

VR equipment

We use Vive Pro and Vive headsets on Windows, Mac and Linux, and simpler Oculus Rift S on Windows. Also use wireless with Vive Pro. Might mention resolution, refresh rate, field of view specs.

Vive Pro HTC wireless adapter Wireless transmitter
Oculus Rift S VR graphics card, Nvidia RTX 2080

Other 3D visualization technologies

Hololens 2 Magic Leap One Oculus Quest Looking Glass

Some new technologies are less ready for research use than VR tethered to a PC.

Older 3D technologies are being discontinued by manufacturers

Tutorials and Examples using ChimeraX VR

From the ChimeraX tutorials web page.

Some UCSF labs using VR

These labs have their own VR equipment and use ChimeraX VR: