VRmol: an integrative web-based virtual reality system to explore macromolecular structure

Applications of visualization technology in the structural sciences

The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data-particularly from cryo-electron microscopy and x-ray crystallography-are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.

Virtual reality in drug design: Benefits, applications and industrial perspectives

Virtual reality (VR) is a tool which has transformative potential in domains which involve the visualization of complex 3D data such as structure-based drug design (SBDD), where it offers new ways to visualize and manipulate complex molecular structures in three dimensions, and enable intuitive exploration of protein-ligand complexes. In this article, we outline three levels of interaction which are available in immersive VR environments for drug discovery, and provide illustrative case studies with applications in COVID-19 research and protein-ligand docking. We discuss VR's role in drug discovery based on conversations with experts from the pharmaceutical industry. While industry experts are mostly optimistic about the potential of VR, they point to the challenges related to integration with existing workflows and the need for improved hardware ergonomics, as well as ensuring a synergistic relationship between VR and an expanding suite of artificial intelligence (AI) tools.

MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality

MolecularWebXR is a new web-based platform for education, science communication and scientific peer discussion in chemistry and biology, based on modern web-based Virtual Reality (VR) and Augmented Reality (AR). With no installs as it is all web-served, MolecularWebXR enables multiple users to simultaneously explore, communicate and discuss concepts about chemistry and biology in immersive 3D environments, by manipulating and passing around objects with their bare hands and pointing at different elements with natural hand gestures. Users may either be present in the same physical space or distributed around the world, in the latter case talking naturally with each other thanks to built-in audio. While MolecularWebXR offers the most immersive experience on high-end AR/VR headsets, its WebXR core also supports participation on consumer devices such as smartphones (with optional cardboard goggles for enhanced immersion), computers, and tablets. MolecularWebXR includes preset VR rooms covering topics in general, inorganic, and organic chemistry, as well as biophysics, structural biology, and general biology. Users can also add new content via the PDB2AR tool. We demonstrate MolecularWebXR's versatility and ease of use across a wide age range (12-80) in fully virtual and mixed real-virtual sessions at science outreach events, undergraduate and graduate courses, scientific collaborations, and conference presentations. MolecularWebXR is available for free use without registration at https://molecularwebxr.org. A blog post version of this preprint with embedded videos is available at https://go.epfl.ch/molecularwebxr-blog-post.

YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities

The industry's transition from three-dimensional (3D) glasses to virtual reality (VR) headsets has left modelers stranded without hardware supply, since walking around and waving arms in a virtual world is a great experience but also very tiring when doing time-intensive modeling work. We present a novel software implementation that uses a VR headset while sitting at a desk in front of the normal screen, which is beamed into the virtual reality together with keyboard, mouse, and chair using the headset's cameras and an extra tracker attached to the seat-back. Compared to 3D glasses, this yields a comparably relaxing but much more immersive workplace and provides additional possibilities such as taking molecules into one's hands, standing up, and walking or teleporting through the models. This VR functionality has been combined with a molecular graphics engine based on Vulkan, a next-generation cross-platform application programming interface (API) for GPUs and the successor of the widely used Open Graphics Library (OpenGL). It is built into the YASARA Model program, which includes many features like small and large molecule builders, electron densities, partial surfaces, contact analysis, coordinate manipulation, and animations. Interactive tutorials are provided to guide modelers into VR and familiarize them with the molecular modeling features. YASARA Model is available for Linux, Windows, Android, and MacOS (the latter without VR) with an introductory video at www.YASARA.org/vr.

Application of Virtual Reality Technology in Clinical Practice, Teaching, and Research in Complementary and Alternative Medicine

Background

The application of virtual reality (VR) in clinical settings is growing rapidly, with encouraging results. As VR has been introduced into complementary and alternative medicine (CAM), a systematic review must be undertaken to understand its current status.

Aim

This review aims to evaluate and summarize the current applications of VR in CAM, as well as to explore potential directions for future research and development.

Methods

After a brief description of VR technology, we discuss the past 20 years of clinical VR applications in the medical field. Then, we discuss the theoretical basis of the combination of VR technology and CAM, the research thus far, and practical factors regarding usability, etc., from the following three main aspects: clinical application, teaching, and scientific research. Finally, we summarize and propose hypotheses on the application of VR in CAM and its limitations.

Results

Our review of the theoretical underpinnings and research findings to date leads to the prediction that VR and CAM will have a significant impact on future research and practice.

Conclusion

Although there is still much research needed to advance the science in this area, we strongly believe that VR applications will become indispensable tools in the toolbox of CAM researchers and practitioners and will only grow in relevance and popularity in the era of digital health.

Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web

Several groups developed in the last years augmented and virtual reality (AR/VR) software to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring expensive hardware. We launched in 2020 moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through commodity web-based AR that works on consumer devices like smartphones, tablets and laptops. Among thousands of users, teachers increasingly request more biological macromolecules to be available, a demand that we cannot address individually. Therefore, to allow users to build their own material, we built a web interface where they can create online AR experiences in few steps starting from Protein Data Bank, AlphaFold or custom uploaded structures, or from virtual objects/scenes exported from the Visual Molecular Dynamics program, without any programming knowledge. The web tool also returns WebXR sessions for viewing and manipulating the models in WebXR-compatible devices including smartphones, tablets, and also immersive VR headsets with WebXR-capable browsers, where models can be manipulated even with bare hands when supported by the device. The tool is accessible for free at https://molecularweb.epfl.ch/pages/pdb2ar.html.

CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data

Single-cell RNAseq is a routinely used method to explore heterogeneity within cell populations. Data from these experiments are often visualized using dimension reduction methods such as UMAP and tSNE, where each cell is projected in two or three dimensional space. Three-dimensional projections can be more informative for larger and complex datasets because they are less prone to merging and flattening similar cell-types/clusters together. However, visualizing and cross-comparing 3D projections using current software on conventional flat-screen displays is far from optimal as they are still essentially 2D, and lack meaningful interaction between the user and the data. Here we present CellexalVR (www.cellexalvr.med.lu.se), a feature-rich, fully interactive virtual reality environment for the visualization and analysis of single-cell experiments that allows researchers to intuitively and collaboratively gain an understanding of their data.

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Single-cell experiments are often visualized when embedded into three dimensions

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CellexalVR is a virtual reality environment to visualize all data simultaneously

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Teams can analyze single-cell experiments together in VR regardless of location

Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions

Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions. In this chapter, we reviewed some of the available tools, highlighting their features, and describing their functions with practical information on their usage.

The VRNetzer platform enables interactive network analysis in Virtual Reality

Networks provide a powerful representation of interacting components within complex systems, making them ideal for visually and analytically exploring big data. However, the size and complexity of many networks render static visualizations on typically-sized paper or screens impractical, resulting in proverbial ‘hairballs’. Here, we introduce a Virtual Reality (VR) platform that overcomes these limitations by facilitating the thorough visual, and interactive, exploration of large networks. Our platform allows maximal customization and extendibility, through the import of custom code for data analysis, integration of external databases, and design of arbitrary user interface elements, among other features. As a proof of concept, we show how our platform can be used to interactively explore genome-scale molecular networks to identify genes associated with rare diseases and understand how they might contribute to disease development. Our platform represents a general purpose, VR-based data exploration platform for large and diverse data types by providing an interface that facilitates the interaction between human intuition and state-of-the-art analysis methods.

Data-rich networks can be difficult to interpret beyond a certain size. Here, the authors introduce a platform that uses virtual reality to allow the visual exploration of large networks, while interfacing with data repositories and other analytical methods to improve the interpretation of big data.

An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19

The era of the explosion of immersive technologies has bumped head-on with the coronavirus disease 2019 (COVID-19) global pandemic caused by the severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2). The proper understanding of the three-dimensional structures that compose the virus, as well as of those involved in the infection process and in treatments, is expected to contribute to the advance of fundamental and applied research against this pandemic, including basic molecular biology studies and drug design. Virtual reality (VR) is a powerful technology to visualize the biomolecular structures that are currently being identified for SARS-CoV-2 infection, opening possibilities to significant advances in the understanding of the disease-associate mechanisms and thus to boost new therapies and treatments. The present availability of VR for a large variety of practical applications together with the increasingly easiness, quality and economic access of this technology is transforming the way we interact with digital information. Here, we review the software implementations currently available for VR visualization of SARS-CoV-2 molecular structures, covering a range of virtual environments: CAVEs, desktop software, and cell phone applications, all of them combined with head-mounted devices like cardboards, Oculus Rift or the HTC Vive. We aim to impulse and facilitate the use of these emerging technologies in research against COVID-19 trying to increase the knowledge and thus minimizing risks before placing huge amounts of money for the development of potential treatments.