Treffer: Elements and roadmap for interactive molecular graphics and modeling "in the Holodeck".
Title:
Elements and roadmap for interactive molecular graphics and modeling "in the Holodeck".
Authors:
Mulholland AJ; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK., Abriata LA; Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Source:
Protein science : a publication of the Protein Society [Protein Sci] 2026 Feb; Vol. 35 (2), pp. e70457.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE
Imprint Name(s):
Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, N.Y. : Cambridge University Press, c1992-
Original Publication: New York, N.Y. : Cambridge University Press, c1992-
MeSH Terms:
References:
Abriata LA. Web apps come of age for molecular sciences. Informatics. Volume 4. Switzerland: MDPI; 2017. p. 28.
Abriata LA. Building blocks for commodity augmented reality‐based molecular visualization and modeling in web browsers. PeerJ Comput Sci. 2020;6:e260.
Abriata LA. Control web apps via natural language by casting speech to commands with GPT‐3. Medium. https://towardsdatascience.com/control-web-apps-via-natural-language-by-casting-speech-to-commands-with-gpt-3-113177f4eab1. 2022.
Abriata LA. The Nobel prize in chemistry: past, present, and future of AI in biology. Commun Biol. 2024;7:1–3.
Abriata LA. The MolecularWeb universe: web‐based, immersive, multiuser molecular graphics and modeling, for education and work in chemistry, structural biology, and materials sciences. Preprint at 2025. https://doi.org/10.48550/arXiv.2509.04056.
Amaro RE, Mulholland AJ. Multiscale methods in drug design bridge chemical and biological complexity in the search for cures. Nat Rev Chem. 2018;2:0148.
Aspuru‐Guzik A, Lindh R, Reiher M. The matter simulation (R)evolution. ACS Cent Sci. 2018;4:144–152.
Baaden M. MolPlay: democratizing interactive molecular simulations and analyses with a portable, turnkey platform. J Phys Chem B. 2024;128:9132–9142.
Baaden M, Glowacki DR. Virtual reality in drug design: benefits, applications and industrial perspectives. Curr Opin Struct Biol. 2025;92:103044.
Batatia I, Benner P, Chiang Y, Elena AM, Kovács DP, Riebesell J, et al. A foundation model for atomistic materials chemistry. Preprint. 2025. https://doi.org/10.48550/arXiv.2401.00096.
Bennie SJ, Ranaghan KE, Deeks H, Goldsmith HE, O'Connor MB, Mulholland AJ, et al. Teaching enzyme catalysis using interactive molecular dynamics in virtual reality. J Chem Educ. 2019;96:2488–2496.
Bozal‐Ginesta C, Pablo‐García S, Choi C, Tarancón A, Aspuru‐Guzik A. Developing machine learning for heterogeneous catalysis with experimental and computational data. Nat Rev Chem. 2025;9:601–616.
Cassidy KC, Šefčík J, Raghav Y, Chang A, Durrant JD. ProteinVR: web‐based molecular visualization in virtual reality. PLoS Comput Biol. 2020;16:e1007747.
Chen Y, Wu Z. A review on ergonomics evaluations of virtual reality. Work. 2023;74:831–841.
Choi J, Nam G, Choi J, Jung Y. A perspective on foundation models in chemistry. JACS Au. 2025;5:1499–1518.
Cortés Rodríguez FJ, Frattini G, Phloi‐Montri S, Pinto Meireles FT, Terrien DA, Cruz‐León S, et al. MolecularWebXR: multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality. J Mol Graph Model. 2025;135:108932.
Crossley‐Lewis J, Dunn J, Buda C, Sunley GJ, Elena AM, Todorov IT, et al. Interactive molecular dynamics in virtual reality for modelling materials and catalysts. J Mol Graph Model. 2023;125:108606.
Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive molecular dynamics in virtual reality is an effective tool for flexible substrate and inhibitor docking to the SARS‐CoV‐2 Main protease. J Chem Inf Model. 2020;60:5803–5814.
Deeks HM, Walters RK, Hare SR, O'Connor MB, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality for accurate flexible protein‐ligand docking. PLoS One. 2020;15:e0228461.
Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug‐protein binding pathways interactively sampled in virtual reality. Sci Rep. 2023;13:16665.
Devereux C, Smith JS, Huddleston KK, Barros K, Zubatyuk R, Isayev O, et al. Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens. J Chem Theory Comput. 2020;16:4192–4202.
Doutreligne S, Cragnolini T, Pasquali S, Derreumaux P, Baaden M. UnityMol: interactive scientific visualization for integrative biology. 2014 IEEE 4th symposium on large data analysis and visualization (LDAV). Paris, France: IEEE; 2014. p. 109–110. https://doi.org/10.1109/LDAV.2014.7013213.
Dunn J, Crossley‐Lewis J, McCluskey AR, Jackson F, Buda C, Sunley GJ, et al. Diffusion mechanisms and preferential dynamics of promoter molecules in ZSM‐5 zeolite. Cat Sci Technol. 2024;14:3674–3681.
Fombona‐Pascual A, Fombona J, Vicente R. Augmented reality, a review of a way to represent and manipulate 3D chemical structures. J Chem Inf Model. 2022;62:1863–1872.
Gao X, Ramezanghorbani F, Isayev O, Smith JS, Roitberg AE. TorchANI: a free and open source PyTorch‐based deep learning implementation of the ANI neural network potentials. J Chem Inf Model. 2020;60:3408–3415.
Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt‐Drake J, Meng EC, et al. Molecular visualization on the Holodeck. J Mol Biol. 2018;430:3982–3996.
Jamieson‐Binnie AD, O'Connor MB, Barnoud J, Wonnacott MD, Bennie SJ, Glowacki DR. Narupa iMD: a VR‐enabled multiplayer framework for streaming interactive molecular simulations. ACM SIGGRAPH 2020 immersive pavilion. New York, NY, USA: Association for Computing Machinery; 2020. p. 1–2. https://doi.org/10.1145/3388536.3407891.
Kaufeld M, Mundt M, Forst S, Hecht H. Optical see‐through augmented reality can induce severe motion sickness. Displays. 2022;74:102283.
Khan Z, Chellappa V, Ginda G. Virtual reality (VR) user interfaces: guidelines for human factors and ergonomic design. 7th European industrial engineering and operations management conference; 2024. https://doi.org/10.46254/EU07.vol.20240127.
Kim E, Shin G. User discomfort while using a virtual reality headset as a personal viewing system for text‐intensive office tasks. Ergonomics. 2021;64:891–899.
Kozlíková B, Krone M, Falk M, Lindow N, Baaden M, Baum D, et al. Visualization of biomolecular structures: state of the art revisited. Comput Graph Forum. 2017;36:178–204. https://doi.org/10.1111/cgf.13072.
Kuťák D, Vázquez P‐P, Isenberg T, Krone M, Baaden M, Byška J, et al. State of the art of molecular visualization in immersive virtual environments. Comput Graph Forum. 2023;42:e14738. https://doi.org/10.1111/cgf.14738.
Martinez X, Chavent M, Baaden M. Visualizing protein structures—tools and trends. Biochem Soc Trans. 2020;48:499–506.
Martinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O'Donoghue S, et al. Molecular graphics: bridging structural biologists and computer scientists. Structure. 2019;27:1617–1623.
Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 2023;32(11):e4792. https://doi.org/10.1002/pro.4792.
Narayanan SM, Braza JD, Griffiths R‐R, Bou A, Wellawatte G, Ramos MC, et al. Training a scientific reasoning model for chemistry. Preprint 2025.
O’Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, et al. Sampling molecular conformations and dynamics in a multiuser virtual reality framework. Sci Adv. 2018;4:eaat2731.
O'Connor MB, Bennie SJ, Deeks HM, Jamieson‐Binnie A, Jones AJ, Shannon RJ, et al. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: an open‐source multi‐person framework. J Chem Phys. 2019;150(22):220901. https://doi.org/10.1063/1.5092590.
O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, et al. Visualizing biological data—now and in the future. Nat Methods. 2010;7:S2–S4.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. Visualization of macromolecular structures. Nat Methods. 2010;7:S42–S55.
Richards G. The origins of the journal. J Mol Graph Model. 2022;117:108301.
Richardson JS, Richardson DC, Goodsell DS. Seeing the PDB. J Biol Chem. 2021;296:100742.
Rodriguez FC, Krapp L, Dal Peraro M, Abriata L. HandMol: Coupling WebXR, AI and HCI technologies for Immersive, Natural, Collaborative and Inclusive Molecular Modeling. 2023.
Rodriguez FC, Krapp L, Meireles FTP, Peraro MD, Abriata L. MolecularWeb democratizes web‐based, immersive, multiuser molecular graphics and modeling. Preprint at 2025. https://doi.org/10.26434/chemrxiv-2025-46. p. 89.
Rodríguez FC, Cortés Rodríguez F, Dualde F, Massiot P, Frattini G, Moreno DM, et al. Updates on moleculARweb, the Swiss portal for chemistry and structural biology education using augmented and now also virtual reality: chemical education. Chimia. 2023;77:264–265.
Rodríguez FC, Dal Peraro M, Abriata LA. Democratizing interactive, immersive experiences for science education with WebXR. Nat Comput Sci. 2021;1:631–632.
Rodríguez FC, Dal Peraro M, Abriata LA. Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web. J Mol Graph Model. 2022;114:108164.
Rodríguez FC, Frattini G, Krapp LF, Martinez‐Hung H, Moreno DM, Roldán M, et al. MoleculARweb: a web site for chemistry and structural biology education through interactive augmented reality out of the box in commodity devices. J Chem Educ. 2021;98:2243–2255.
Rodríguez FC, Krapp LF, Dal Peraro M, Abriata LA. Visualization, interactive handling and simulation of molecules in commodity augmented reality in web browsers using moleculARweb's virtual modeling kits. Chimia. 2022;76:145–150.
Roebuck Williams R, Barnoud J, Toledo L, Holzapfel T, Glowacki DR. Measuring the limit of perception of bond stiffness of interactive molecules in VR via a gamified psychophysics experiment. In: de Paolis LT, Arpaia P, Sacco M, editors. Extended reality. Volume 15027. Cham, Switzerland: Springer Nature; 2024. p. 190–198.
Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, et al. Mol* viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 2021;49:W431–W437.
Seifrid M, Pollice R, Aguilar‐Granda A, Chan ZM, Hotta K, Ser CT, et al. Autonomous chemical experiments: challenges and perspectives on establishing a self‐driving lab. Acc Chem Res. 2022;55:2454–2466. https://doi.org/10.1021/acs.accounts.2c00220.
Shannon RJ, Deeks HM, Burfoot E, Clark E, Jones AJ, Mulholland AJ, et al. Exploring human‐guided strategies for reaction network exploration: interactive molecular dynamics in virtual reality as a tool for citizen scientists. J Chem Phys. 2021;155:154106.
Smith GR, Bello C, Bialic‐Murphy L, Clark E, Delavaux CS, Fournier de Lauriere C, et al. Ten simple rules for using large language models in science, version 1.0. PLoS Comput Biol. 2024;20:e1011767.
Smith JS, Isayev O, Roitberg AE. ANI‐1: an extensible neural network potential with DFT accuracy at force field computational cost. Chem Sci. 2017;8:3192–3203.
Stroud HJ, Wonnacott MD, Barnoud J, Roebuck Williams R, Dhouioui M, McSloy A, et al. NanoVer server: a Python package for serving real‐time multi‐user interactive molecular dynamics in virtual reality. J Open Source Softw. 2025;10:8118.
Suardíaz R, Siddiqui SA, Kwon H, van der Kamp MW, González‐Sánchez L, Moody PCE, et al. Solvent channels and electric fields guide proton delivery to the active site of heme peroxidases. Angew Chem. 2025;64:e202515743.
Todd H, Emsley P. Development and assessment of CootVR, a virtual reality computer program for model building. Acta Crystallogr Sect D Struct Biol. 2021;77:19–27.
Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. The emerging potential of interactive virtual reality in drug discovery. Expert Opin Drug Discovery. 2022a;17:685–698.
Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. Interactivity: the missing link between virtual reality technology and drug discovery pipelines. Preprint at 2022b. https://doi.org/10.48550/arXiv.2202.03953.
Williams RR, Varcoe X, Glowacki BR, Gale EM, Jamieson‐Binnie A, Glowacki DR. Subtle sensing: detecting differences in the flexibility of virtually simulated molecular objects. Extended abstracts of the 2020 CHI conference on human factors in computing systems (CHI EA '20). New York, NY, USA: Association for Computing Machinery; 2020. p. 1–8. https://doi.org/10.1145/3334480.3383026.
Xu K, Liu N, Xu J, Guo C, Zhao L, Wang HW, et al. VRmol: an integrative web‐based virtual reality system to explore macromolecular structure. Bioinformatics. 2021;37:1029–1031.
Abriata LA. Building blocks for commodity augmented reality‐based molecular visualization and modeling in web browsers. PeerJ Comput Sci. 2020;6:e260.
Abriata LA. Control web apps via natural language by casting speech to commands with GPT‐3. Medium. https://towardsdatascience.com/control-web-apps-via-natural-language-by-casting-speech-to-commands-with-gpt-3-113177f4eab1. 2022.
Abriata LA. The Nobel prize in chemistry: past, present, and future of AI in biology. Commun Biol. 2024;7:1–3.
Abriata LA. The MolecularWeb universe: web‐based, immersive, multiuser molecular graphics and modeling, for education and work in chemistry, structural biology, and materials sciences. Preprint at 2025. https://doi.org/10.48550/arXiv.2509.04056.
Amaro RE, Mulholland AJ. Multiscale methods in drug design bridge chemical and biological complexity in the search for cures. Nat Rev Chem. 2018;2:0148.
Aspuru‐Guzik A, Lindh R, Reiher M. The matter simulation (R)evolution. ACS Cent Sci. 2018;4:144–152.
Baaden M. MolPlay: democratizing interactive molecular simulations and analyses with a portable, turnkey platform. J Phys Chem B. 2024;128:9132–9142.
Baaden M, Glowacki DR. Virtual reality in drug design: benefits, applications and industrial perspectives. Curr Opin Struct Biol. 2025;92:103044.
Batatia I, Benner P, Chiang Y, Elena AM, Kovács DP, Riebesell J, et al. A foundation model for atomistic materials chemistry. Preprint. 2025. https://doi.org/10.48550/arXiv.2401.00096.
Bennie SJ, Ranaghan KE, Deeks H, Goldsmith HE, O'Connor MB, Mulholland AJ, et al. Teaching enzyme catalysis using interactive molecular dynamics in virtual reality. J Chem Educ. 2019;96:2488–2496.
Bozal‐Ginesta C, Pablo‐García S, Choi C, Tarancón A, Aspuru‐Guzik A. Developing machine learning for heterogeneous catalysis with experimental and computational data. Nat Rev Chem. 2025;9:601–616.
Cassidy KC, Šefčík J, Raghav Y, Chang A, Durrant JD. ProteinVR: web‐based molecular visualization in virtual reality. PLoS Comput Biol. 2020;16:e1007747.
Chen Y, Wu Z. A review on ergonomics evaluations of virtual reality. Work. 2023;74:831–841.
Choi J, Nam G, Choi J, Jung Y. A perspective on foundation models in chemistry. JACS Au. 2025;5:1499–1518.
Cortés Rodríguez FJ, Frattini G, Phloi‐Montri S, Pinto Meireles FT, Terrien DA, Cruz‐León S, et al. MolecularWebXR: multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality. J Mol Graph Model. 2025;135:108932.
Crossley‐Lewis J, Dunn J, Buda C, Sunley GJ, Elena AM, Todorov IT, et al. Interactive molecular dynamics in virtual reality for modelling materials and catalysts. J Mol Graph Model. 2023;125:108606.
Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive molecular dynamics in virtual reality is an effective tool for flexible substrate and inhibitor docking to the SARS‐CoV‐2 Main protease. J Chem Inf Model. 2020;60:5803–5814.
Deeks HM, Walters RK, Hare SR, O'Connor MB, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality for accurate flexible protein‐ligand docking. PLoS One. 2020;15:e0228461.
Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug‐protein binding pathways interactively sampled in virtual reality. Sci Rep. 2023;13:16665.
Devereux C, Smith JS, Huddleston KK, Barros K, Zubatyuk R, Isayev O, et al. Extending the applicability of the ANI deep learning molecular potential to sulfur and halogens. J Chem Theory Comput. 2020;16:4192–4202.
Doutreligne S, Cragnolini T, Pasquali S, Derreumaux P, Baaden M. UnityMol: interactive scientific visualization for integrative biology. 2014 IEEE 4th symposium on large data analysis and visualization (LDAV). Paris, France: IEEE; 2014. p. 109–110. https://doi.org/10.1109/LDAV.2014.7013213.
Dunn J, Crossley‐Lewis J, McCluskey AR, Jackson F, Buda C, Sunley GJ, et al. Diffusion mechanisms and preferential dynamics of promoter molecules in ZSM‐5 zeolite. Cat Sci Technol. 2024;14:3674–3681.
Fombona‐Pascual A, Fombona J, Vicente R. Augmented reality, a review of a way to represent and manipulate 3D chemical structures. J Chem Inf Model. 2022;62:1863–1872.
Gao X, Ramezanghorbani F, Isayev O, Smith JS, Roitberg AE. TorchANI: a free and open source PyTorch‐based deep learning implementation of the ANI neural network potentials. J Chem Inf Model. 2020;60:3408–3415.
Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt‐Drake J, Meng EC, et al. Molecular visualization on the Holodeck. J Mol Biol. 2018;430:3982–3996.
Jamieson‐Binnie AD, O'Connor MB, Barnoud J, Wonnacott MD, Bennie SJ, Glowacki DR. Narupa iMD: a VR‐enabled multiplayer framework for streaming interactive molecular simulations. ACM SIGGRAPH 2020 immersive pavilion. New York, NY, USA: Association for Computing Machinery; 2020. p. 1–2. https://doi.org/10.1145/3388536.3407891.
Kaufeld M, Mundt M, Forst S, Hecht H. Optical see‐through augmented reality can induce severe motion sickness. Displays. 2022;74:102283.
Khan Z, Chellappa V, Ginda G. Virtual reality (VR) user interfaces: guidelines for human factors and ergonomic design. 7th European industrial engineering and operations management conference; 2024. https://doi.org/10.46254/EU07.vol.20240127.
Kim E, Shin G. User discomfort while using a virtual reality headset as a personal viewing system for text‐intensive office tasks. Ergonomics. 2021;64:891–899.
Kozlíková B, Krone M, Falk M, Lindow N, Baaden M, Baum D, et al. Visualization of biomolecular structures: state of the art revisited. Comput Graph Forum. 2017;36:178–204. https://doi.org/10.1111/cgf.13072.
Kuťák D, Vázquez P‐P, Isenberg T, Krone M, Baaden M, Byška J, et al. State of the art of molecular visualization in immersive virtual environments. Comput Graph Forum. 2023;42:e14738. https://doi.org/10.1111/cgf.14738.
Martinez X, Chavent M, Baaden M. Visualizing protein structures—tools and trends. Biochem Soc Trans. 2020;48:499–506.
Martinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O'Donoghue S, et al. Molecular graphics: bridging structural biologists and computer scientists. Structure. 2019;27:1617–1623.
Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 2023;32(11):e4792. https://doi.org/10.1002/pro.4792.
Narayanan SM, Braza JD, Griffiths R‐R, Bou A, Wellawatte G, Ramos MC, et al. Training a scientific reasoning model for chemistry. Preprint 2025.
O’Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, et al. Sampling molecular conformations and dynamics in a multiuser virtual reality framework. Sci Adv. 2018;4:eaat2731.
O'Connor MB, Bennie SJ, Deeks HM, Jamieson‐Binnie A, Jones AJ, Shannon RJ, et al. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: an open‐source multi‐person framework. J Chem Phys. 2019;150(22):220901. https://doi.org/10.1063/1.5092590.
O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, et al. Visualizing biological data—now and in the future. Nat Methods. 2010;7:S2–S4.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. Visualization of macromolecular structures. Nat Methods. 2010;7:S42–S55.
Richards G. The origins of the journal. J Mol Graph Model. 2022;117:108301.
Richardson JS, Richardson DC, Goodsell DS. Seeing the PDB. J Biol Chem. 2021;296:100742.
Rodriguez FC, Krapp L, Dal Peraro M, Abriata L. HandMol: Coupling WebXR, AI and HCI technologies for Immersive, Natural, Collaborative and Inclusive Molecular Modeling. 2023.
Rodriguez FC, Krapp L, Meireles FTP, Peraro MD, Abriata L. MolecularWeb democratizes web‐based, immersive, multiuser molecular graphics and modeling. Preprint at 2025. https://doi.org/10.26434/chemrxiv-2025-46. p. 89.
Rodríguez FC, Cortés Rodríguez F, Dualde F, Massiot P, Frattini G, Moreno DM, et al. Updates on moleculARweb, the Swiss portal for chemistry and structural biology education using augmented and now also virtual reality: chemical education. Chimia. 2023;77:264–265.
Rodríguez FC, Dal Peraro M, Abriata LA. Democratizing interactive, immersive experiences for science education with WebXR. Nat Comput Sci. 2021;1:631–632.
Rodríguez FC, Dal Peraro M, Abriata LA. Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web. J Mol Graph Model. 2022;114:108164.
Rodríguez FC, Frattini G, Krapp LF, Martinez‐Hung H, Moreno DM, Roldán M, et al. MoleculARweb: a web site for chemistry and structural biology education through interactive augmented reality out of the box in commodity devices. J Chem Educ. 2021;98:2243–2255.
Rodríguez FC, Krapp LF, Dal Peraro M, Abriata LA. Visualization, interactive handling and simulation of molecules in commodity augmented reality in web browsers using moleculARweb's virtual modeling kits. Chimia. 2022;76:145–150.
Roebuck Williams R, Barnoud J, Toledo L, Holzapfel T, Glowacki DR. Measuring the limit of perception of bond stiffness of interactive molecules in VR via a gamified psychophysics experiment. In: de Paolis LT, Arpaia P, Sacco M, editors. Extended reality. Volume 15027. Cham, Switzerland: Springer Nature; 2024. p. 190–198.
Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, et al. Mol* viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 2021;49:W431–W437.
Seifrid M, Pollice R, Aguilar‐Granda A, Chan ZM, Hotta K, Ser CT, et al. Autonomous chemical experiments: challenges and perspectives on establishing a self‐driving lab. Acc Chem Res. 2022;55:2454–2466. https://doi.org/10.1021/acs.accounts.2c00220.
Shannon RJ, Deeks HM, Burfoot E, Clark E, Jones AJ, Mulholland AJ, et al. Exploring human‐guided strategies for reaction network exploration: interactive molecular dynamics in virtual reality as a tool for citizen scientists. J Chem Phys. 2021;155:154106.
Smith GR, Bello C, Bialic‐Murphy L, Clark E, Delavaux CS, Fournier de Lauriere C, et al. Ten simple rules for using large language models in science, version 1.0. PLoS Comput Biol. 2024;20:e1011767.
Smith JS, Isayev O, Roitberg AE. ANI‐1: an extensible neural network potential with DFT accuracy at force field computational cost. Chem Sci. 2017;8:3192–3203.
Stroud HJ, Wonnacott MD, Barnoud J, Roebuck Williams R, Dhouioui M, McSloy A, et al. NanoVer server: a Python package for serving real‐time multi‐user interactive molecular dynamics in virtual reality. J Open Source Softw. 2025;10:8118.
Suardíaz R, Siddiqui SA, Kwon H, van der Kamp MW, González‐Sánchez L, Moody PCE, et al. Solvent channels and electric fields guide proton delivery to the active site of heme peroxidases. Angew Chem. 2025;64:e202515743.
Todd H, Emsley P. Development and assessment of CootVR, a virtual reality computer program for model building. Acta Crystallogr Sect D Struct Biol. 2021;77:19–27.
Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. The emerging potential of interactive virtual reality in drug discovery. Expert Opin Drug Discovery. 2022a;17:685–698.
Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. Interactivity: the missing link between virtual reality technology and drug discovery pipelines. Preprint at 2022b. https://doi.org/10.48550/arXiv.2202.03953.
Williams RR, Varcoe X, Glowacki BR, Gale EM, Jamieson‐Binnie A, Glowacki DR. Subtle sensing: detecting differences in the flexibility of virtually simulated molecular objects. Extended abstracts of the 2020 CHI conference on human factors in computing systems (CHI EA '20). New York, NY, USA: Association for Computing Machinery; 2020. p. 1–8. https://doi.org/10.1145/3334480.3383026.
Xu K, Liu N, Xu J, Guo C, Zhao L, Wang HW, et al. VRmol: an integrative web‐based virtual reality system to explore macromolecular structure. Bioinformatics. 2021;37:1029–1031.
Contributed Indexing:
Keywords: AI agents; WebXR; artificial intelligence; augmented reality (AR); collaboration; extended reality (XR); human‐computer interaction; interactive molecular dynamics; large language models; mixed reality; molecular graphics; molecular manipulation; molecular modeling; multi‐modal interaction; protein science; structural biology; virtual reality (VR)
Entry Date(s):
Date Created: 20260120 Date Completed: 20260120 Latest Revision: 20260122
Update Code:
20260122
PubMed Central ID:
PMC12817468
DOI:
10.1002/pro.70457
PMID:
41556555
Database:
MEDLINE
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Molecular graphics have been instrumental in advancing chemistry, drug discovery, materials science and structural biology, enabling visualization of molecular systems from static images to dynamic web displays and immersive platforms. While effective visualization is largely a solved problem, in this perspective we argue that the next significant leap lies beyond passive viewing. Rather, the frontier is in enabling intuitive, immersive, direct 3D manipulation and interaction with molecular systems to address the inherent limitations of carrying out complex 3D tasks via 2D interfaces. The vision, which is starting to be realized, is of immersive molecular science environments in which researchers leverage multi-modal inputs that feel natural (with hands plus possibly haptic or pseudo-haptic feedback, voice user interfaces and AI-based assistance), collaborating seamlessly in concurrent sessions, naturally visualizing and connecting different types of data and models, and engaging with molecules assisted by real-time simulation engines. Many of the technologies required to develop such environments already exist, at least in basic forms. In this Perspective, we discuss current prototypes and software solutions that incorporate some of the elements needed, and that are available for use. We discuss applications and practical demonstrations, and outline the developments that are required to make the Molecular Holodeck a reality. We also discuss challenges that need to be addressed in order to achieve this vision. The coming shift toward hands-on, multiuser, immersive, natural and physics-informed manipulation will transform hypothesis generation, molecular design, fundamental understanding, collaborative working, discussions, and thus research and education in the chemical sciences, as others have envisioned for "molecular visualization in the holodeck."
(© 2026 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)