Virtual Reality at UCSF

Site under construction July 13, 2018

News

Research Applications

Drug binding sites
Matt Jacobson lab
Weekly group meetings using VR to analyze ligand binding using ChimeraX. Contact Wilian Cortopassi Coelho.
p97 inhibitors
Michelle Arkin lab
Inhibitors of p97 involved in protein recycling and possibly neurodegnerative disease. Virtual reality demonstration for UCSF Campaign.
Antibiotic resistance
Danica Fujimori lab
Mechanism of post-translational methylation of a ribosome nucleotide causing antibiotic resistance. Shown in VR for Byer's award reception.
Cell motility 3D light microscopy
Dyche Mullins lab
ChimeraX VR displays 3D microscopy time series. Neutrophils crawling through collagen filaments.
Calcium signaling in neurons
Bo Huang lab
Dan Xie observes calcium signaling in 8000 zebrafish neurons using 3d light-sheet microscopy time series. Demonstrated in VR for Byer's award lecture using ChimeraX VR.
Neurodegeneration in zebrafish
Steve Finkbeiner lab
Neurodegeneration in zebrafish in 3d light microscopy time series from Jeremy Linsley at Glastone Institute shown with ConfocalVR.
DNA origami virtual lab
Shawn Douglas lab
Interview with Shawn on the Foo Show about his VR nano-machine lab simulation.
Brain disorder treatment
Adam Gazzaley lab
Neuroscape.

VR Equipment and Software

Shared VR equipment
Tom Ferrin lab

An HTC Vive virtual reality headset for viewing your molecular structures or microscopy data is available at the Visualization Vault in Genentech Hall at UCSF Mission Bay. Contact Tom Goddard.

ChimeraX VR
Tom Ferrin lab

The ChimeraX visualization package can display atomic structures and microscopy data with the vr command. A tutorial explores mutations in a scorpion toxin.

Collaborative structure viewing
Tom Ferrin lab

ChimeraX VR meeting command allows multiperson viewing of structures and microscopy data.

Molecular Zoo
Alan Brilliant in Tom Ferrin lab

Molecular Zoo is a biomolecule education VR program that lets children handle fully flexible molecules of life: water, aspirin, saturated fat, carbon dioxide, caffeine, ATP.

ConfocalVR
Tom Skillman and Caroline Stefani at Benaroya Research Insitute

ConfocalVR displays multichannel 3D light microscopy data.

Protein Databank VR viewer
Tom Skillman at Benaroya Research Institute

AltPDB collaborative viewing of Protein Databank molecular structures.

Projects

Virtual Reality in the San Francisco Public Libraries - pre-proposal to setup VR systems for informal STEM education in the 27 branches of the San Francisco public library. Full proposal due November 17, 2018.

Analysis of Molecules and Cells in Virtual Reality - proposal to setup research VR systems in 5 UCSF labs for cryoEM structure refinement, 3D light microscopy, and multi-person VR collaborations. Under review. July 2018.

Exploring Drug Binding using Molecular Dynamics and Virtual Reality - proposal by Tom Goddard, Wilian Cortopassi Coelho, Matt Jacobson, Michael Grabe, Tristan Croll, and Tom Ferrin to study mutations effecting drug binding sites. Funded. January 2018.

Virtual Reality Molecular Playground - proposal for STEM education VR application to familiarize students with biomolecules. Not funded. January 2017.

People

Alan Brilliant (UCSC) - Developer of Molecular Zoo biomolecule education application.

Wilian Cortopassi Coelho (UCSF) - Studies drug-receptor interactions using VR in Matt Jacobson's lab. Publishing 3 drug studies in July 2018 using VR analysis.

Shawn Douglas (UCSF) - Developed VR lab simulation for DNA origami research.

Tom Ferrin (UCSF) - Provides shared HTC Vive VR equipment in the Visualization Vault.

Christopher Fortney (NIH) - Manages the Virtual Reality Consulting Service at the NIH library.

Tom Goddard (UCSF) - ChimeraX VR developer.

Matt Jacobson (UCSF) - Analyzes drug binding, weekly use of VR in group meetings.

Meghan McCarthy (NIH) - Using ChimeraX VR with radiologists at NIH.

Dyche Mullins (UCSF) - VR visualization 3D light microscopy of crawling neutrophil cells.

Tom Skillman (Immersive Science) - Founder of Immersive Science, developing VR science applications ConfocalVR for light microscopy, AltPDB for collaborative molecular structure viewing, and FCS-VR for flow cytometry analysis.

Caroline Stefani (Benaroya Research Institute) - Developer of ConfocalVR for light microscopy, working with Tom Skillman.

James Tyrwhitt-Drake - Developer of speech recognition command input from ChimeraX. Worked with Meghan McCarthy at NIH virtual reality applications.

References


Tom Goddard / UCSF / goddard@cgl.ucsf.edu