Research ArticleAPPLIED SCIENCES AND ENGINEERING

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

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Science Advances  29 Jun 2018:
Vol. 4, no. 6, eaat2731
DOI: 10.1126/sciadv.aat2731
  • Fig. 1 Technical schematic of the HTC Vive VR setup that we designed to carry out the studies outlined here.

    Bottom: Two users within the multiperson VR framework passing a simulated C60 molecule back and forth. Each user’s position is determined using a real-time optical tracking system composed of synchronized infrared light sources. Each user’s VR HMD is rendered locally on a computer fitted with a suitable GPU; MD calculations and maintenance of global user position data take place on a separate server, which can be cloud-mounted. As long as the network connecting the client and server enables sufficiently fast data transfer, system latency is imperceptible to the human senses. Top: Single-person setup, where the user is chaperoning a real-time GPU-accelerated MD simulation to generate an association pathway that docks a benzylpenicillin ligand (magenta) into a binding pose on the TEM-1 β-lactamase enzyme.

  • Fig. 2 Experimental iMS tasks.

    Experimental iMS user studies featured the following tasks: (i) threading CH4 through a nanotube, (ii) changing the screw sense of a helicene molecule, and (iii) tying a knot in a polypeptide (17-ALA). Colors selected in this figure are chosen for the sake of clarity.

  • Fig. 3 User study results.

    Left-hand panel shows user accomplishment rates for the tasks outlined in Fig. 2 (n = 32 for all tasks), with Poisson error estimates. Right-hand panel shows the corresponding distribution of task accomplishment times, along with box-and-whisker plots. Whiskers indicate the data range, and box limits indicate the standard error of the distribution. The mean is shown as a solid line, and the median is shown as a dashed line.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/6/eaat2731/DC1

    section S1. Launching a cloud-hosted iMD session

    section S2. User study data

    section S3. Platform design

    section S4. Qualitative analysis of participants’ subjective feedback

    fig. S1. Distribution of round-trip latencies, measured from Bristol to each of the cloud data centers.

    fig. S2. User study results.

    fig. S3. Screenshots of a user’s view from within VR carrying out the nanotube task.

    fig. S4. User’s view of the molecular manipulation application when using either a mouse or touchscreen.

    fig. S5. Number of participants (y axis) self-reporting their attitudes on the importance of depth perception, navigating the virtual space, and controlling molecules with two hands.

    table S1. Self-reported familiarity with the VR and tablet platforms on a Likert scale.

    movie S1. Sampling molecular conformational dynamics in VR (www.vimeo.com/244670465).

    movie S2. Interactively sampling dynamical pathways of benzylpenicillin binding to β-lactamase (www.vimeo.com/235894288).

  • Supplementary Materials

    This PDF file includes:

    • section S1. Launching a cloud-hosted iMD session
    • section S2. User study data
    • section S3. Platform design
    • section S4. Qualitative analysis of participants’ subjective feedback
    • fig. S1. Distribution of round-trip latencies, measured from Bristol to each of the cloud data centers.
    • fig. S2. User study results.
    • fig. S3. Screenshots of a user’s view from within VR carrying out the nanotube task.
    • fig. S4. User’s view of the molecular manipulation application when using either a mouse or touchscreen.
    • fig. S5. Number of participants (y axis) self-reporting their attitudes on the importance of depth perception, navigating the virtual space, and controlling molecules with two hands.
    • table S1. Self-reported familiarity with the VR and tablet platforms on a Likert scale.

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    Other Supplementary Material for this manuscript includes the following:

    • movie S1 (.mp4 format). Sampling molecular conformational dynamics in VR (www.vimeo.com/244670465).
    • movie S2 (.mp4 format). Interactively sampling dynamical pathways of benzylpenicillin binding to β-lactamase (www.vimeo.com/235894288).

    Files in this Data Supplement:

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