State of the Art of Molecular Visualization in Immersive Virtual Environments

Kuťák, David; Vázquez, Pere‐Pau; Isenberg, Tobias; Krone, Michael; Baaden, Marc; Byška, Jan; Kozlíková, Barbora; Miao, Haichao

doi:10.1111/cgf.14738

Title: State of the Art of Molecular Visualization in Immersive Virtual Environments

Journal Article · Fri Feb 24 00:00:00 EST 2023 · Computer Graphics Forum

DOI:https://doi.org/10.1111/cgf.14738· OSTI ID:1958690

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^[2]; Isenberg, Tobias ^[3];

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Visitlab, Masaryk University Brno Czech Republic, AIT Austrian Institute of Technology Vienna Austria
ViRVIG group, Universitat Politècnica de Catalunya Barcelona Spain
Université Paris‐Saclay, CNRS, Inria, LISN Paris France
Department of Computer Science and Engineering Tandon School of Engineering, New York University New York United States, Big Data Visual Analytics, University of Tübingen Tübingen Germany
Laboratoire de Biochimie Théorique, UPR 9080 CNRS Paris France
Visitlab, Masaryk University Brno Czech Republic, Department of Informatics University of Bergen Bergen Norway
Visitlab, Masaryk University Brno Czech Republic
Center for Applied Scientific Computing, Lawrence Livermore National Laboratory Livermore California USA

Abstract 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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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); Spanish Ministerio de Economía y Competitividad; French National Research Agency; Carl Zeiss Stiftung; Ministerio de Ciencia e Innovación

Grant/Contract Number:: LLNL‐LDRD 22‐FS‐026; AC52-07NA27344; ANR-21-CE45-0014; ANR-11-LABX-0011; ANR-11-EQPX-0008

OSTI ID:: 1958690

Alternate ID(s):: OSTI ID: 1958692; OSTI ID: 1973195

Report Number(s):: LLNL-JRNL-847822; e14738

Journal Information:: Computer Graphics Forum, Journal Name: Computer Graphics Forum Vol. 42 Journal Issue: 6; ISSN 0167-7055

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (140)

Virtual Reality: Beyond Visualization El Beheiry, Mohamed; Doutreligne, Sébastien; Caporal, Clément Journal of Molecular Biology, Vol. 431, Issue 7 https://doi.org/10.1016/j.jmb.2019.01.033	journal	March 2019
Augmented reality in scientific visualization and communications: a new dawn of looking at antibody interactions Chan, Kwok-Fong; Poh, Jun-Jie; Wu, Wei-Ling Antibody Therapeutics, Vol. 3, Issue 3 https://doi.org/10.1093/abt/tbaa021	journal	July 2020
Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion Skanberg, Robin; Vazquez, Pere-Pau; Guallar, Victor IEEE Transactions on Visualization and Computer Graphics, Vol. 22, Issue 1 https://doi.org/10.1109/TVCG.2015.2467293	journal	January 2016
Visual Analysis of Biomolecular Cavities: State of the Art Krone, M.; Kozlíková, B.; Lindow, N. Computer Graphics Forum, Vol. 35, Issue 3 https://doi.org/10.1111/cgf.12928	journal	June 2016
Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures Miao, Haichao; De Llano, Elisa; Sorger, Johannes IEEE Transactions on Visualization and Computer Graphics, Vol. 24, Issue 1 https://doi.org/10.1109/TVCG.2017.2743981	journal	January 2018
Cybersickness in current-generation virtual reality head-mounted displays: systematic review and outlook Caserman, Polona; Garcia-Agundez, Augusto; Gámez Zerban, Alvar Virtual Reality, Vol. 25, Issue 4 https://doi.org/10.1007/s10055-021-00513-6	journal	April 2021
ProteinVR: Web-based molecular visualization in virtual reality Cassidy, Kevin C.; Šefčík, Jan; Raghav, Yogindra PLOS Computational Biology, Vol. 16, Issue 3 https://doi.org/10.1371/journal.pcbi.1007747	journal	March 2020
Exploring 3-D virtual reality technology for spatial ability and chemistry achievement Merchant, Z.; Goetz, E. T.; Keeney-Kennicutt, W. Journal of Computer Assisted Learning, Vol. 29, Issue 6 https://doi.org/10.1111/jcal.12018	journal	June 2013
Pondering the Concept of Abstraction in (Illustrative) Visualization Viola, Ivan; Isenberg, Tobias IEEE Transactions on Visualization and Computer Graphics, Vol. 24, Issue 9 https://doi.org/10.1109/TVCG.2017.2747545	journal	September 2018
VRmol: an integrative web-based virtual reality system to explore macromolecular structure Xu, Kui; Liu, Nan; Xu, Jingle Bioinformatics, Vol. 37, Issue 7 https://doi.org/10.1093/bioinformatics/btaa696	journal	August 2020
Enhancing visualization of molecular simulations using sonification Rau, Benjamin; Friess, Florian; Krone, Michael 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR) https://doi.org/10.1109/VARMS.2015.7151725	conference	March 2015
Development and assessment of CootVR, a virtual reality computer program for model building Todd, Hamish; Emsley, Paul Acta Crystallographica Section D Structural Biology, Vol. 77, Issue 1 https://doi.org/10.1107/S2059798320013625	journal	January 2021
Virtual structure reconstruction and energy estimation of a peptide from a physical tangible interface Martinez, Xavier; Ferey, Nicolas; Vezien, Jean-Marc 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR) https://doi.org/10.1109/VARMS.2015.7151724	conference	March 2015
Viewing geometric protein structures from inside a CAVE Akkiraju, N.; Edelsbrunner, H. IEEE Computer Graphics and Applications, Vol. 16, Issue 4 https://doi.org/10.1109/38.511855	journal	July 1996
Co-Coot: A real-time collaborative tool for bio-molecular modeling and visualization Lee, Jun; Kang, Lin-Woo; Kim, HyungSeok 2011 IEEE International Symposium on VR Innovation https://doi.org/10.1109/ISVRI.2011.5759651	conference	March 2011
Seven Myths on Crowding and Peripheral Vision Strasburger, Hans i-Perception, Vol. 11, Issue 3 https://doi.org/10.1177/2041669520913052	journal	May 2020
A never-ending story in the sky: The secrets of chemical evolution Puzzarini, Cristina; Barone, Vincenzo Physics of Life Reviews, Vol. 32 https://doi.org/10.1016/j.plrev.2019.07.001	journal	March 2020
Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments Alharbi, Ruwayda; Strnad, Ondrej; Luidolt, Laura R. IEEE Transactions on Visualization and Computer Graphics, Vol. 29, Issue 3 https://doi.org/10.1109/TVCG.2021.3133592	journal	March 2023
Molecular Surface Maps Krone, Michael; Friess, Florian; Scharnowski, Katrin IEEE Transactions on Visualization and Computer Graphics, Vol. 23, Issue 1 https://doi.org/10.1109/TVCG.2016.2598824	journal	January 2017
Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering Stone, John E.; Sherman, William R.; Schulten, Klaus 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) https://doi.org/10.1109/IPDPSW.2016.121	conference	May 2016
Empirical Studies in Information Visualization: Seven Scenarios Lam, H.; Bertini, E.; Isenberg, P. IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 9 https://doi.org/10.1109/TVCG.2011.279	journal	September 2012
Exploring DrugBank in Virtual Reality Chemical Space Probst, Daniel; Reymond, Jean-Louis Journal of Chemical Information and Modeling, Vol. 58, Issue 9 https://doi.org/10.1021/acs.jcim.8b00402	journal	August 2018
Flipping the laboratory: improving student engagement and learning outcomes in second year science courses Loveys, Beth R.; Riggs, Karina M. International Journal of Science Education, Vol. 41, Issue 1 https://doi.org/10.1080/09500693.2018.1533663	journal	October 2018
Molecular Graphics: Bridging Structural Biologists and Computer Scientists Martinez, Xavier; Krone, Michael; Alharbi, Naif Structure, Vol. 27, Issue 11 https://doi.org/10.1016/j.str.2019.09.001	journal	November 2019
Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking Deeks, Helen M.; Walters, Rebecca K.; Hare, Stephanie R. PLOS ONE, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pone.0228461	journal	March 2020
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments Martinez, Xavier; Baaden, Marc Acta Crystallographica Section D Structural Biology, Vol. 77, Issue 6 https://doi.org/10.1107/S2059798321002941	journal	May 2021
Immersive virtual reality in the age of the Metaverse: A hybrid-narrative review based on the technology affordance perspective Dincelli, Ersin; Yayla, Alper The Journal of Strategic Information Systems, Vol. 31, Issue 2 https://doi.org/10.1016/j.jsis.2022.101717	journal	June 2022
A novel virtual environment for molecular system design Alsayegh, Rajab; Paramonov, Leonid; Makatsoris, Charalampos 2013 IEEE International Conference on Computational Intelligence and Virtual Environments for Measurement Systems and Applications (CIVEMSA) https://doi.org/10.1109/CIVEMSA.2013.6617392	conference	July 2013
Interactive Drug Design in Virtual Reality Tse, Ching-Man; Li, Hongjian; Leung, Kwong-Sak 2011 15th International Conference on Information Visualisation https://doi.org/10.1109/IV.2011.72	conference	July 2011
Molecular Genomics Education Through Gamified Cell Exploration in Virtual Reality Patterson, Kate; Lilja, Andrew; Arrebola, Mark Proceedings of the 17th International Conference on Virtual-Reality Continuum and its Applications in Industry https://doi.org/10.1145/3359997.3365724	conference	November 2019
Immersive VR for scientific visualization: a progress report Simpson, R. M.; LaViola, J. J.; Laidlaw, D. H. IEEE Computer Graphics and Applications, Vol. 20, Issue 6 https://doi.org/10.1109/38.888006	journal	January 2000
Immersive Intelligence Genomic Data Visualisation Lau, Chng Wei; Nguyen, Quang Vinh; Qu, Zhonglin ACSW 2019: Australasian Computer Science Week 2019, Proceedings of the Australasian Computer Science Week Multiconference https://doi.org/10.1145/3290688.3290722	conference	January 2019
Augmented Reality and Virtual Reality Displays: Perspectives and Challenges Zhan, Tao; Yin, Kun; Xiong, Jianghao iScience, Vol. 23, Issue 8 https://doi.org/10.1016/j.isci.2020.101397	journal	August 2020
The eyes have it: a task by data type taxonomy for information visualizations Shneiderman, B. Proceedings 1996 IEEE Symposium on Visual Languages https://doi.org/10.1109/VL.1996.545307	conference	January 1996
Fast, Simple, Student Generated Augmented Reality Approach for Protein Visualization in the Classroom and Home Study Argüello, José M.; Dempski, Robert E. Journal of Chemical Education, Vol. 97, Issue 8 https://doi.org/10.1021/acs.jchemed.0c00323	journal	June 2020
iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene GigaScience, Vol. 6, Issue 8 https://doi.org/10.1093/gigascience/gix054	journal	July 2017
What do you do when two hands are not enough? interactive selection of bonds between pairs of tangible molecules Maier, Patrick; Tonnis, Marcus; Klinker, Gudrun 2010 IEEE Symposium on 3D User Interfaces (3DUI) https://doi.org/10.1109/3DUI.2010.5444716	conference	March 2010
Exploring Chemistry with Wireless, PC-Less Portable Virtual Reality Laboratories Qin, Tina; Cook, Matt; Courtney, Matt Journal of Chemical Education, Vol. 98, Issue 2 https://doi.org/10.1021/acs.jchemed.0c00954	journal	December 2020
Collaborative Work in Augmented Reality: A Survey Sereno, Mickael; Wang, Xiyao; Besancon, Lonni IEEE Transactions on Visualization and Computer Graphics https://doi.org/10.1109/TVCG.2020.3032761	journal	January 2020
Optimised Molecular Graphics on the HoloLens Muller, Christoph; Braun, Matthias; Ertl, Thomas 2019 IEEE Conference on Virtual Reality and 3D User Interfaces (VR) https://doi.org/10.1109/VR.2019.8798111	conference	March 2019
Extended reality applications in industry 4.0. – A systematic literature review Adriana Cárdenas-Robledo, Leonor; Hernández-Uribe, Óscar; Reta, Carolina Telematics and Informatics, Vol. 73 https://doi.org/10.1016/j.tele.2022.101863	journal	September 2022
Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures Kozlíková, B.; Krone, M.; Falk, M. Computer Graphics Forum, Vol. 36, Issue 8 https://doi.org/10.1111/cgf.13072	journal	November 2016
A Collaborative Virtual Reality Environment for Molecular Biology Lee, Jun; Quy, PhamSy; Kim, Jee-In 2009 International Symposium on Ubiquitous Virtual Reality https://doi.org/10.1109/ISUVR.2009.14	conference	July 2009
The ImmersaDesk and Infinity Wall projection-based virtual reality displays Czernuszenko, Marek; Pape, Dave; Sandin, Daniel ACM SIGGRAPH Computer Graphics, Vol. 31, Issue 2 https://doi.org/10.1145/271283.271303	journal	May 1997
Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations Jamieson-Binnie, Alexander D.; O'Connor, Michael B.; Barnoud, Jonathan ACM SIGGRAPH 2020 Immersive Pavilion https://doi.org/10.1145/3388536.3407891	conference	August 2020
An idea to explore: Use of augmented reality for teaching three‐dimensional biomolecular structures Peterson, Celeste N.; Tavana, Sara Z.; Akinleye, Olukemi P. Biochemistry and Molecular Biology Education, Vol. 48, Issue 3 https://doi.org/10.1002/bmb.21341	journal	March 2020
A head-mounted three dimensional display Sutherland, Ivan E. Proceedings of the December 9-11, 1968, fall joint computer conference, part I on - AFIPS '68 (Fall, part I) https://doi.org/10.1145/1476589.1476686	conference	January 1968
A practical guide to developing virtual and augmented reality exercises for teaching structural biology: VR and AR for Teaching Structural Biology Garcia-Bonete, Maria-Jose; Jensen, Maja; Katona, Gergely Biochemistry and Molecular Biology Education, Vol. 47, Issue 1 https://doi.org/10.1002/bmb.21188	journal	November 2018
ProMVR - Protein Multiplayer Virtual Reality Tool Xu, Tianshu; Yallapragada, Venkata VB; Tangney, Mark Proceedings of the 27th ACM Symposium on Virtual Reality Software and Technology https://doi.org/10.1145/3489849.3489935	conference	December 2021
Instant Construction and Visualization of Crowded Biological Environments Klein, Tobias; Autin, Ludovic; Kozlikova, Barbora IEEE Transactions on Visualization and Computer Graphics, Vol. 24, Issue 1 https://doi.org/10.1109/TVCG.2017.2744258	journal	January 2018
Real-Time Interactive Simulation and Visualization of Organic Molecules Gandhi, Heta A.; Jakymiw, Sebastian; Barrett, Rainier Journal of Chemical Education, Vol. 97, Issue 11 https://doi.org/10.1021/acs.jchemed.9b01161	journal	September 2020
Eukaryo: An AR and VR Application for Cell Biology Yuen, Douglas; Santoso, Markus; Cartwright, Stephen International Journal of Virtual Reality, Vol. 16, Issue 1 https://doi.org/10.20870/IJVR.2016.16.1.2877	journal	January 2016
Virtual and augmented reality as spatial ability training tools Dünser, Andreas; Steinbügl, Karin; Kaufmann, Hannes Proceedings of the 6th ACM SIGCHI New Zealand chapter's international conference on Computer-human interaction design centered HCI - CHINZ '06 https://doi.org/10.1145/1152760.1152776	conference	January 2006
Study of Commodity VR for Computational Material Sciences Hagita, Katsumi; Matsumoto, Shigenori; Ota, Koji ACS Omega, Vol. 4, Issue 2 https://doi.org/10.1021/acsomega.8b03483	journal	February 2019
BiochemAR: An Augmented Reality Educational Tool for Teaching Macromolecular Structure and Function Sung, Rou-Jia; Wilson, Andrew T.; Lo, Stanley M. Journal of Chemical Education, Vol. 97, Issue 1 https://doi.org/10.1021/acs.jchemed.8b00691	journal	December 2019
Visualizing 3D Molecular Structures Using an Augmented Reality App Eriksen, Kristina; Nielsen, Bjarne E.; Pittelkow, Michael Journal of Chemical Education, Vol. 97, Issue 5 https://doi.org/10.1021/acs.jchemed.9b01033	journal	April 2020
Exploring Data in Virtual Reality Millais, Patrick; Jones, Simon L.; Kelly, Ryan Extended Abstracts of the 2018 CHI Conference on Human Factors in Computing Systems https://doi.org/10.1145/3170427.3188537	conference	April 2018
NOMAD VR: Multiplatform virtual reality viewer for chemistry simulations García-Hernández, Rubén Jesús; Kranzlmüller, Dieter Computer Physics Communications, Vol. 237 https://doi.org/10.1016/j.cpc.2018.11.013	journal	April 2019
Development and use of augmented reality models to teach medicinal chemistry Smith, Chase; Friel, Carolyn J. Currents in Pharmacy Teaching and Learning, Vol. 13, Issue 8 https://doi.org/10.1016/j.cptl.2021.06.008	journal	August 2021
An Immersive Visualization Study on Molecules Manipulation da Costa, Luis Antonio L. F.; Nedel, Luciana Porcher 2017 19th Symposium on Virtual and Augmented Reality (SVR) https://doi.org/10.1109/SVR.2017.30	conference	November 2017
MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices Rodríguez, Fabio Cortés; Frattini, Gianfranco; Krapp, Lucien F. Journal of Chemical Education, Vol. 98, Issue 7 https://doi.org/10.1021/acs.jchemed.1c00179	journal	June 2021
VSEPR Theory, An Interactive and Immersive Virtual Reality Fujiwara, Danica; Kellar, Kevin; Humer, Irene 2020 6th International Conference of the Immersive Learning Research Network (iLRN) https://doi.org/10.23919/iLRN47897.2020.9155185	conference	June 2020
Molecular Visualization on the Holodeck Goddard, Thomas D.; Brilliant, Alan A.; Skillman, Thomas L. Journal of Molecular Biology, Vol. 430, Issue 21 https://doi.org/10.1016/j.jmb.2018.06.040	journal	October 2018
Immersive design of DNA molecules with a tangible interface Schkolne, S.; Ishii, H.; Schroder, P. IEEE Visualization 2004 https://doi.org/10.1109/VISUAL.2004.47	conference	January 2004
Tasks, Techniques, and Tools for Genomic Data Visualization Nusrat, S.; Harbig, T.; Gehlenborg, N. Computer Graphics Forum, Vol. 38, Issue 3 https://doi.org/10.1111/cgf.13727	journal	June 2019
VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality Brůža, Vojtěch; Byška, Jan; Mičan, Jan Computers & Graphics, Vol. 98 https://doi.org/10.1016/j.cag.2021.06.009	journal	August 2021
Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality Bennie, Simon J.; Ranaghan, Kara E.; Deeks, Helen Journal of Chemical Education, Vol. 96, Issue 11 https://doi.org/10.1021/acs.jchemed.9b00181	journal	July 2019
Does gamification improve student learning outcome? Evidence from a meta-analysis and synthesis of qualitative data in educational contexts Bai, Shurui; Hew, Khe Foon; Huang, Biyun Educational Research Review, Vol. 30 https://doi.org/10.1016/j.edurev.2020.100322	journal	June 2020
UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules Doutreligne, Sebastien; Gageat, Cedric; Cragnolini, Tristan 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR) https://doi.org/10.1109/VARMS.2015.7151718	conference	March 2015
Understanding differences between combinations of 2D and 3D input and output devices for 3D data visualization Wang, Xiyao; Besançon, Lonni; Ammi, Mehdi International Journal of Human-Computer Studies, Vol. 163 https://doi.org/10.1016/j.ijhcs.2022.102820	journal	July 2022
A Protein in the palm of your hand through augmented reality Berry, Colin; Board, Jason Biochemistry and Molecular Biology Education, Vol. 42, Issue 5 https://doi.org/10.1002/bmb.20805	journal	June 2014
Visual Analysis of Large‐Scale Protein‐Ligand Interaction Data Schatz, Karsten; Franco‐Moreno, Juan José; Schäfer, Marco Computer Graphics Forum, Vol. 40, Issue 6 https://doi.org/10.1111/cgf.14386	journal	August 2021
LearnDNA Sharma, Lakshmi; Jin, Rong; Prabhakaran, Balakrishnan Proceedings of the 3rd International Workshop on Interactive and Spatial Computing https://doi.org/10.1145/3191801.3191810	conference	April 2018
Using virtual reality for drug discovery: a promising new outlet for novel leads Liu, Xiao-Huan; Wang, Tao; Lin, Jian-Ping Expert Opinion on Drug Discovery, Vol. 13, Issue 12 https://doi.org/10.1080/17460441.2018.1546286	journal	November 2018
Learning molecular biology by VR playing Lu, Bf; Lim, Kt; Zheng, Jm Proceedings of the 2004 ACM SIGGRAPH international conference on Virtual Reality continuum and its applications in industry - VRCAI '04 https://doi.org/10.1145/1044588.1044622	conference	January 2004
A compact, wide-FOV optical design for head-mounted displays Rakkolainen, Ismo; Turk, Matthew; Höllerer, Tobias Proceedings of the 22nd ACM Conference on Virtual Reality Software and Technology https://doi.org/10.1145/2993369.2996322	conference	November 2016
Investigating the Nature of Students' Reasoning in Connecting Molecular Structures of Stereoisomers with their Physical Properties Using an AR App K. L., Narasimha Swamy; Dasgupta, Chandan 2018 IEEE Tenth International Conference on Technology for Education (T4E) https://doi.org/10.1109/T4E.2018.00018	conference	December 2018
Scale Trotter: Illustrative Visual Travels Across Negative Scales Halladjian, Sarkis; Miao, Haichao; Kouril, David IEEE Transactions on Visualization and Computer Graphics, Vol. 26, Issue 1 https://doi.org/10.1109/TVCG.2019.2934334	journal	January 2020
Pepblock Builder VR – An Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design Yallapragada, Venkata V. B.; Xu, Tianshu; Walker, Sidney P. Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.674211	journal	May 2021
Survey of Immersive Analytics Fonnet, Adrien; Prie, Yannick IEEE Transactions on Visualization and Computer Graphics, Vol. 27, Issue 3 https://doi.org/10.1109/TVCG.2019.2929033	journal	March 2021
An accessible, open‐source mobile application for macromolecular visualization using augmented reality Lee, Ning Yuan; Tucker‐Kellogg, Greg Biochemistry and Molecular Biology Education, Vol. 48, Issue 3 https://doi.org/10.1002/bmb.21335	journal	February 2020
ProteinScanAR - An Augmented Reality Web Application for High School Education in Biomolecular Life Sciences Nickels, Stefan; Sminia, Hienke; Mueller, Sabine C. 2012 16th International Conference on Information Visualisation https://doi.org/10.1109/IV.2012.97	conference	July 2012
RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality Borrel, Alexandre; Fourches, Denis Bioinformatics, Vol. 33, Issue 23 https://doi.org/10.1093/bioinformatics/btx485	journal	August 2017
Ionic and Metallic Bonding Visualization Using Augmented Reality Rostianingsih, Silvica; Setiawan, Alexander; Halim, Christopher Imantaka 2018 3rd Technology Innovation Management and Engineering Science International Conference (TIMES-iCON) https://doi.org/10.1109/TIMES-iCON.2018.8621665	conference	December 2018
CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments Gardner, Adam; Autin, Ludovic; Barbaro, Brett IEEE Computer Graphics and Applications, Vol. 38, Issue 6 https://doi.org/10.1109/MCG.2018.2877076	journal	November 2018
Dynamic Virtual Proteins: Visualization, Interaction and Collaboration in Virtual Reality Gauthier, Jean-Marc; McGrath, Ian; Suresh Patel, Jagdish 25th ACM Symposium on Virtual Reality Software and Technology https://doi.org/10.1145/3359996.3365050	conference	November 2019
VR in chemistry, a review of scientific research on advanced atomic/molecular visualization Fombona-Pascual, Alba; Fombona, Javier; Vázquez-Cano, Esteban Chemistry Education Research and Practice, Vol. 23, Issue 2 https://doi.org/10.1039/d1rp00317h	journal	January 2022
Developing and Using BioSIM^AR, an Augmented Reality Program to Visualize and Learn about Chemical Structures in a Virtual Environment on Any Internet-Connected Device Fernandes, Henrique S.; Cerqueira, Nuno M. F. S. A.; Sousa, Sérgio F. Journal of Chemical Education, Vol. 98, Issue 5 https://doi.org/10.1021/acs.jchemed.0c01317	journal	April 2021
HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models Kouril, David; Isenberg, Tobias; Kozlikova, Barbora IEEE Transactions on Visualization and Computer Graphics, Vol. 27, Issue 8 https://doi.org/10.1109/TVCG.2020.2975583	journal	August 2021
Learning with augmented reality: Impact of dimensionality and spatial abilities Krüger, Jule M.; Palzer, Kevin; Bodemer, Daniel Computers and Education Open, Vol. 3 https://doi.org/10.1016/j.caeo.2021.100065	journal	December 2022
ChemPreview : an augmented reality-based molecular interface Zheng, Min; Waller, Mark P. Journal of Molecular Graphics and Modelling, Vol. 73 https://doi.org/10.1016/j.jmgm.2017.01.019	journal	May 2017
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization Byška, J.; Trautner, T.; Marques, S. M. Computer Graphics Forum, Vol. 38, Issue 3 https://doi.org/10.1111/cgf.13701	journal	June 2019
Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS Laureanti, Joseph; Brandi, Juan; Offor, Elvis Protein Science, Vol. 29, Issue 1 https://doi.org/10.1002/pro.3773	journal	November 2019
Designing and Implementing VR²E²C, a Virtual Reality Remote Education for Experimental Chemistry System Lu, Yihua; Xu, Yao; Zhu, Xi Journal of Chemical Education, Vol. 98, Issue 8 https://doi.org/10.1021/acs.jchemed.1c00439	journal	July 2021
3D Printing of Molecular Models Gardner, Adam; Olson, Arthur Journal of Biocommunication, Vol. 40, Issue 1 https://doi.org/10.5210/jbc.v40i1.6626	journal	February 2016
Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges Lv, Zhihan; Tek, Alex; Da Silva, Franck PLoS ONE, Vol. 8, Issue 3 https://doi.org/10.1371/journal.pone.0057990	journal	March 2013
Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures Kutak, David; Selzer, Matias Nicolas; Byska, Jan IEEE Transactions on Visualization and Computer Graphics, Vol. 28, Issue 12 https://doi.org/10.1109/TVCG.2021.3106328	journal	December 2022
Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework O’Connor, Michael B.; Bennie, Simon J.; Deeks, Helen M. The Journal of Chemical Physics, Vol. 150, Issue 22 https://doi.org/10.1063/1.5092590	journal	June 2019
Visualizing large-scale atomistic simulations in ultra-resolution immersive environments Reda, Khairi; Knoll, Aaron; Nomura, Ken-ichi 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) https://doi.org/10.1109/LDAV.2013.6675159	conference	October 2013
Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data Salvadori, Andrea; Del Frate, Gianluca; Pagliai, Marco International Journal of Quantum Chemistry, Vol. 116, Issue 22 https://doi.org/10.1002/qua.25207	journal	July 2016
Virtual and augmented reality for biomedical applications Venkatesan, Mythreye; Mohan, Harini; Ryan, Justin R. Cell Reports Medicine, Vol. 2, Issue 7 https://doi.org/10.1016/j.xcrm.2021.100348	journal	July 2021
Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web Cortés Rodríguez, Fabio; Dal Peraro, Matteo; Abriata, Luciano A. Journal of Molecular Graphics and Modelling, Vol. 114 https://doi.org/10.1016/j.jmgm.2022.108164	journal	July 2022
Chemical Exploration with Virtual Reality in Organic Teaching Laboratories Ferrell, Jonathon B.; Campbell, Joseph P.; McCarthy, Dillon R. Journal of Chemical Education, Vol. 96, Issue 9 https://doi.org/10.1021/acs.jchemed.9b00036	journal	July 2019
Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules Leinen, Philipp; Green, Matthew F. B.; Esat, Taner Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.220	journal	November 2015
LifeBrush: Painting, simulating, and visualizing dense biomolecular environments Davison, Timothy; Samavati, Faramarz; Jacob, Christian Computers & Graphics, Vol. 82 https://doi.org/10.1016/j.cag.2019.05.006	journal	August 2019
Learning organic chemistry with virtual reality Ramirez, Jorge Alvarez; Bueno, Ana Maria Villarreal 2020 IEEE International Conference on Engineering Veracruz (ICEV) https://doi.org/10.1109/ICEV50249.2020.9289672	conference	October 2020
GPU-powered tools boost molecular visualization Chavent, M.; Levy, B.; Krone, M. Briefings in Bioinformatics, Vol. 12, Issue 6 https://doi.org/10.1093/bib/bbq089	journal	February 2011
Effects of Immersion on Visual Analysis of Volume Data Laha, B.; Sensharma, K.; Schiffbauer, J. D. IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 4 https://doi.org/10.1109/TVCG.2012.42	journal	April 2012
Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer Balo, Aidin R.; Wang, Merry; Ernst, Oliver P. Nature Methods, Vol. 14, Issue 12 https://doi.org/10.1038/nmeth.4506	journal	December 2017
CSynth: an interactive modelling and visualization tool for 3D chromatin structure Todd, Stephen; Todd, Peter; McGowan, Simon J. Bioinformatics, Vol. 37, Issue 7 https://doi.org/10.1093/bioinformatics/btaa757	journal	August 2020
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease Deeks, Helen M.; Walters, Rebecca K.; Barnoud, Jonathan Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c01030	journal	November 2020
Journey to the centre of the cell: Virtual reality immersion into scientific data Johnston, Angus P. R.; Rae, James; Ariotti, Nicholas Traffic, Vol. 19, Issue 2 https://doi.org/10.1111/tra.12538	journal	November 2017
iBET: Immersive visualization of biological electron-transfer dynamics Nakano, C. Masato; Moen, Erick; Byun, Hye Suk Journal of Molecular Graphics and Modelling, Vol. 65 https://doi.org/10.1016/j.jmgm.2016.02.009	journal	April 2016
Towards an Understanding of Augmented Reality Extensions for Existing 3D Data Analysis Tools Wang, Xiyao; Besançon, Lonni; Rousseau, David Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems https://doi.org/10.1145/3313831.3376657	conference	April 2020
Development of a virtual reality platform for effective communication of structural data in drug discovery Kingsley, Laura J.; Brunet, Vincent; Lelais, Gerald Journal of Molecular Graphics and Modelling, Vol. 89 https://doi.org/10.1016/j.jmgm.2019.03.010	journal	June 2019
Eukaryo Yuen, Douglas; Cartwright, Stephen; Jacob, Christian Proceedings of the 2016 Virtual Reality International Conference https://doi.org/10.1145/2927929.2927931	conference	March 2016
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes Juárez-Jiménez, Jordi; Tew, Philip; O′Connor, Michael Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c00221	journal	November 2020
Teaching Biochemistry and Molecular Biology with Virtual Reality — Lesson Creation and Student Response Coan, Heather; Goehle, Geoff; Youker, Robert Journal of Teaching and Learning, Vol. 14, Issue 1 https://doi.org/10.22329/jtl.v14i1.6234	journal	May 2020
ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening Sabando, Maria Virginia; Ulbrich, Pavol; Selzer, Matias IEEE Transactions on Visualization and Computer Graphics, Vol. 27, Issue 2 https://doi.org/10.1109/TVCG.2020.3030438	journal	February 2021
Towards An Understanding of Mobile Touch Navigation in a Stereoscopic Viewing Environment for 3D Data Exploration Lopez, David; Oehlberg, Lora; Doger, Candemir IEEE Transactions on Visualization and Computer Graphics, Vol. 22, Issue 5 https://doi.org/10.1109/TVCG.2015.2440233	journal	May 2016
Immersive environment for molecular visualization to interaction between research groups geographically dispersed Correa, Moacyr Francischetti; Schpector, Julio Zukerman; Trevelin, Luis Carlos 2010 3rd International Symposium on Applied Sciences in Biomedical and Communication Technologies (ISABEL 2010) https://doi.org/10.1109/ISABEL.2010.5702889	conference	November 2010
Peppy: A virtual reality environment for exploring the principles of polypeptide structure Doak, David G.; Denyer, Gareth S.; Gerrard, Juliet A. Protein Science, Vol. 29, Issue 1 https://doi.org/10.1002/pro.3752	journal	November 2019
UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3235	journal	September 2017
MOF-VR: A Virtual Reality Program for Performing and Visualizing Immersive Molecular Dynamics Simulations of Guest Molecules in Metal–Organic Frameworks von Wedelstedt, Alexander; Goebel, Gunther; Kalies, Grit Journal of Chemical Information and Modeling, Vol. 62, Issue 5 https://doi.org/10.1021/acs.jcim.2c00158	journal	February 2022
Visual Data Mining by Virtual Reality for Protein-Protein Interaction Networks Aouaa, Noureddine; Gherbi, Rachid; Meziane, Abdelkrim 2018 IEEE/ACS 15th International Conference on Computer Systems and Applications (AICCSA) https://doi.org/10.1109/AICCSA.2018.8612849	conference	October 2018
Wielding the power of interactive molecular simulations Lanrezac, André; Férey, Nicolas; Baaden, Marc WIREs Computational Molecular Science, Vol. 12, Issue 4 https://doi.org/10.1002/wcms.1594	journal	December 2021
InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics Seritan, Stefan; Wang, Yuanheng; Ford, Jason E. Journal of Chemical Education, Vol. 98, Issue 11 https://doi.org/10.1021/acs.jchemed.1c00654	journal	October 2021
Virtual reality: A survey of enabling technologies and its applications in IoT Hu, Miao; Luo, Xianzhuo; Chen, Jiawen Journal of Network and Computer Applications, Vol. 178 https://doi.org/10.1016/j.jnca.2020.102970	journal	March 2021
Interacting with Three-Dimensional Molecular Structures Using an Augmented Reality Mobile App Aw, Jonah Kailer; Boellaard, Kevin Christopher; Tan, Teck Kiang Journal of Chemical Education, Vol. 97, Issue 10 https://doi.org/10.1021/acs.jchemed.0c00387	journal	August 2020
Molecular Rift: Virtual Reality for Drug Designers Norrby, Magnus; Grebner, Christoph; Eriksson, Joakim Journal of Chemical Information and Modeling, Vol. 55, Issue 11 https://doi.org/10.1021/acs.jcim.5b00544	journal	November 2015
Immersive sonification of protein surface Bouchara, Tifanie; Montes, Matthieu 2020 IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (VRW) https://doi.org/10.1109/VRW50115.2020.00082	conference	March 2020
Game-Engine-Assisted Research platform for Scientific computing (GEARS) in Virtual Reality Horton, Brandon K.; Kalia, Rajiv K.; Moen, Erick SoftwareX, Vol. 9 https://doi.org/10.1016/j.softx.2019.01.009	journal	January 2019
Virtual Reality in Chemistry Ihlenfeldt, W. -D. Journal of Molecular Modeling, Vol. 3, Issue 9 https://doi.org/10.1007/s008940050056	journal	September 1997
Sampling molecular conformations and dynamics in a multiuser virtual reality framework O’Connor, Michael; Deeks, Helen M.; Dawn, Edward Science Advances, Vol. 4, Issue 6 https://doi.org/10.1126/sciadv.aat2731	journal	June 2018
An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19 Calvelo, Martín; Piñeiro, Ángel; Garcia-Fandino, Rebeca Computational and Structural Biotechnology Journal, Vol. 18 https://doi.org/10.1016/j.csbj.2020.09.018	journal	January 2020
Identifying the Characteristics of Virtual Reality Gamification for Complex Educational Topics Falah, Jannat; Wedyan, Mohammad; Alfalah, Salsabeel F. M. Multimodal Technologies and Interaction, Vol. 5, Issue 9 https://doi.org/10.3390/mti5090053	journal	September 2021
Molecular visualization in chemistry education: the role of multidisciplinary collaboration Jones, Loretta L.; Jordan, Kenneth D.; Stillings, Neil A. Chem. Educ. Res. Pract., Vol. 6, Issue 3 https://doi.org/10.1039/B5RP90005K	journal	January 2005
Interactive visual analytics of molecular data in immersive environments via a semantic definition of the content and the context Trellet, Mikael; Ferey, Nicolas; Baaden, Marc 2016 Workshop on Immersive Analytics (IA) https://doi.org/10.1109/IMMERSIVE.2016.7932383	conference	March 2016
StereoChem: Augmented Reality 3D Molecular Model Visualization App for Teaching and Learning Stereochemistry Swamy K. L., Narasimha; Chavan, Pankaj S.; Murthy, Sahana 2018 IEEE 18th International Conference on Advanced Learning Technologies (ICALT) https://doi.org/10.1109/ICALT.2018.00065	conference	July 2018
The CAVE: audio visual experience automatic virtual environment Cruz-Neira, Carolina; Sandin, Daniel J.; DeFanti, Thomas A. Communications of the ACM, Vol. 35, Issue 6 https://doi.org/10.1145/129888.129892	journal	June 1992

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