Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations

Jamieson-Binnie, Alexander; O’Connor, Michael B.; Barnoud, Jonathan; Wonnacott, Mark; Bennie, Simon J.; Glowacki, David R.

doi:10.1145/3388536.3407891

Cited by 15 publications

(10 citation statements)

References 2 publications

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“…Narupa, the software framework that we have developed, is open source and uses commodity VR hardware, which is widely accessible. 29 , 34 , 36 , 52 , 53 It can therefore readily be used. We make our Mpro structures and simulations here freely available ( Files S2, S3, S4, and S5 ); these can be used for ligand discovery and structure–activity studies for SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 99%

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

Deeks

Walters

Barnoud

et al. 2020

J. Chem. Inf. Model.

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The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets ( 32160194 PLoS One 2020 15 e0228461 ). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.

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Section: Discussionmentioning

confidence: 99%

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

Deeks

Walters

Barnoud

et al. 2020

J. Chem. Inf. Model.

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“…VRChem and AltPDB. − In addition, some of the available virtual environments were not originally designed for use in educational practice (e.g., ChimeraX), which makes them complicated to interact with . A search for a free immersive virtual environment with molecular dynamics lead to Narupa iMD . Contrary to other available VR environments, a key feature of Narupa iMD is is the modeling of the dynamic state of molecules in real time (in accordance with thermodynamic laws), “bringing molecular dynamics to life” in an immersive way.…”

Section: Methodsmentioning

confidence: 99%

“…75 A search for a free immersive virtual environment with molecular dynamics lead to Narupa iMD. 76 Contrary to other available VR environments, a key feature of Narupa iMD is is the modeling of the dynamic state of molecules in real time (in accordance with thermodynamic laws), "bringing molecular dynamics to life" in an immersive way. Students can manipulate a chemical object by rotating and moving it within the scene.…”

Section: Narupamentioning

confidence: 99%

Implementation of Eye-Tracking Recording Tool into Narupa iMD VR Environment for Application in Chemistry Education

Kuzminov,

Vokhmin,

Sharaeva

et al. 2023

J. Chem. Educ.

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Application of modern technologies, including virtual reality (VR) and eye-tracking (ET), to educational practice has been vigorously researched over the past decade with a focus on enhancing and improving school and university educational process and students' results. The main aim of this technological report is to describe an implementation of a novel toolkit for tracking eye movements in a VR headset. The toolkit is implemented in Narupa iMD�an environment that allows visualizing molecular dynamics and interactions in VR for chemistry education. The toolkit is flexible and can be adapted to other VR environments and for subject areas other than chemistry. The HTC Vive Pro Eye was chosen as a headmounted display (HMD) which supports eye-tracking. The toolkit is designed to primarily work with that device, but can be adapted to other HMDs with ET module. The current report describes a step-by-step process of developing and implementing the software to track eye movements during the learning process. We discuss future prospects for usage of this technology in research and educational practice.

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“…Narupa [ODD*18, OBD*19, DWH*20, JBOB*20] is an open‐source software package where multiple users can cohabit in the same VR space and interact with real‐time molecular simulations. It is based on the iMD‐VR software framework and extends its functionality by enabling a multi‐person VR experience, setting up and customizing interactive user manipulation with MD simulations, and running the application on a local network.…”

Section: Tasksmentioning

confidence: 99%

State of the Art of Molecular Visualization in Immersive Virtual Environments

Kuťák

Vázquez

Isenberg

et al. 2023

Computer Graphics Forum

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Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.

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Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations

Cited by 15 publications

References 2 publications

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

Implementation of Eye-Tracking Recording Tool into Narupa iMD VR Environment for Application in Chemistry Education

State of the Art of Molecular Visualization in Immersive Virtual Environments

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