3DGV: Immersive Exploration of 3D Genome Structures using Virtual Reality

Zhang, E.; Drogaris, Chrisostomos; Guedon, A.; Sossin, Aaron; Faraj, R.; Chen, H.; Cyr, Y.; Majewski, Jacek; Blanchette, Mathieu; Waldispühl, Jérôme

doi:10.1101/855379

Cited by 2 publications

(2 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some of the earliest explorations of VR were focused on molecular visualization [48]. In some approaches, the user's role is primarily observational [2], [21], in others, the user can navigate in a virtual space and inspect a molecular structure from different angles [32], [50], [67], [68]. This is the case in Molecular Rift [46], an immersive and interactive 3D visualization tool for drug design, which involves a molecular viewer controlled by gesture recognition [24].…”

Section: Molecular Modeling and Visualization In Vrmentioning

confidence: 99%

“…ADN Viewer [28] is an application for the visualization and exploration of genomic 3D structures that also integrates VR capabilities to enable stereoscopic visualization on large screens [27]. 3DGV [67] is a newer approach that focuses on manipulating data in two-controller immersive environments, but again it does not support modeling tasks.…”

Section: Molecular Modeling and Visualization In Vrmentioning

confidence: 99%

See 1 more Smart Citation

Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

Kuťák

Selzer

Ganuza

et al. 2022

IEEE Trans. Visual. Comput. Graphics

View full text Add to dashboard Cite

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.

show abstract