Molecular Visualization on the Holodeck

Abstract

Can virtual reality be useful for visualizing and analyzing molecular structures and 3-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 school children about biomolecules that are the machinery of life. What are the advantages and disadvantages of virtual reality for these applications? 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. We describe unique aspects of VR user interfaces, and the software and hardware advances needed for this technology to come into routine use for scientific data analysis.

iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

“…The annotations in iCn3D could also be retrieved by other tools. In the future, iCn3D may adopt emerging 3D technologies such as virtual reality (Goddard, et al, 2018; Goddard, et al, 2018; Olson, 2018).…”

“…With the widespread availability of powerful personal computers and mobile devices, the visualization of biomolecular 3D structure (Kozlikova, et al, 2017; Sali, et al, 2015) is no longer restricted to stand-alone 3D viewer applications such as Chimera (Goddard, et al, 2018; Pettersen, et al, 2004), PyMol (Schrödinger, 2015), or Cn3D (Wang, et al, 2000), which all require the installation of a dedicated application. Interactive visualization of large molecular structures can now be achieved via web-based 3D viewers such as NGL (Rose, et al, 2018; Rose and Hildebrand, 2015), LiteMol (Sehnal, et al, 2017), or Aquaria (O’Donoghue, et al, 2015).…”

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

“…They can also provide intuitive filtering by direct selection of data features or removing unchanged or irrelevant data [98]. The potential augmentation of the user's interactions is also being explored via AR, VR and CAVEs with haptic controllers [99], for example with cutting planes for inspection of VR models.…”

“…Other tools integrate modeling and visualization of 3D from Hi-C: HiC-3Dviewer displays matrix and 3D side-by-side [141]; 3Dgnome provides an analytical suite which can output 3D [142]; 3Disease Browser integrates disease-associated data for comparison [143]; also of note, a number of prototypes propose how such 3D data may be explored in VR [99,124,144]. Finally three further examples expand on this by taking distinct routes to an integrative model.…”

VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure

“…However, structural analysis by AltPDB protein-viewer is complicated due to the need to generate molecular models beforehand by thirdparty tools. UCSF ChimeraX [16,17] also provides certain simple VR interactive functions for structure visualization, but it is mainly designed for a native desktop environment and timeconsuming to learn. In addition, some favorable structural analysis options, like molecules docking and scene sharing, are inaccessible in the VR environment of ChimeraX.…”