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J Mol Biol. 2018 Oct 19;430(21):3982-3996. doi: 10.1016/j.jmb.2018.06.040. Epub 2018 Jun 28.

Molecular Visualization on the Holodeck.

Author information

1
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA. Electronic address: Thomas.Goddard@ucsf.edu.
2
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
3
Benaroya Research Institute, Seattle, WA 98101, USA.
4
AltspaceVR, Redwood City, CA 94063, USA.
5
Bioinformatics and Computational Biosciences Branch, NIH National Institute of Allergy and Infectious Disease, Rockville, MD 20852, USA.

Abstract

Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching schoolchildren about biomolecules that are the machinery of life. Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. Investigations over three decades have produced an extensive literature evaluating the potential of VR in research and education. Consumer VR headsets are now affordable to researchers and educators, allowing direct tests of whether the technology is valuable in these areas. We survey here advantages and disadvantages of VR for molecular biology in the context of affordable and dramatically more powerful VR and graphics hardware than has been available in the past.

KEYWORDS:

AltPDB; ChimeraX; Molecular Zoo; microscopy; virtual reality

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