Treffer: Mol* web molecular graphics engine.
Title:
Mol* web molecular graphics engine.
Authors:
Rose AS; Research Collaboratory for Structural Bioinformatics (RCSB), San Diego Supercomputer Center, University of California San Diego, San Diego, California, USA., Tomasello G; 3D Protein Imaging, Caronno Varesino, Italy., Kovács ÁS; Technische Universität Wien, Vienna, Austria., Autin L; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA., Sehnal D; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom.
Source:
Protein science : a publication of the Protein Society [Protein Sci] 2026 Apr; Vol. 35 (4), pp. e70514.
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:
Allen Institute. Vol‐E, v2.15.0. 2025 https://vol-e.allencell.org/.
Autin L, Barbaro BA, Jewett AI, Ekman A, Verma S, Olson AJ, et al. Integrative structural modelling and visualisation of a cellular organelle. QRB Discov. 2022;3:e11. https://doi.org/10.1017/qrd.2022.10.
Bavoil L, Myers K. Order independent transparency with dual depth peeling. NVIDIA OpenGL SDK. 2008;10(12):2–4. https://developer.download.nvidia.com/SDK/10/opengl/src/dual_depth_peeling/doc/DualDepthPeeling.pdf.
Bekker GJ, Nakamura H, Kinjo AR. Molmil: a molecular viewer for the PDB and beyond. J Chem. 2016;8:42. https://doi.org/10.1186/s13321-016-0155-1.
Beliu G, Altrichter S, Guixà‐González R, Hemberger M, Brauer I, Dahse AK, et al. Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain. Mol Cell. 2021;81(5):905–921.E5. https://doi.org/10.1016/j.molcel.2020.12.042.
Černý J, Malý M, Božíková P, Prchalová T, Svoboda J, Biedermannová L, et al. DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis. Nucleic Acids Res. 2026;54(1):gkaf1491. https://doi.org/10.1093/nar/gkaf1491.
Dobson L, Gerdán C, Tusnády S, Szekeres L, Kuffa K, Langó T, et al. UniTmp: unified resources for transmembrane proteins. Nucleic Acids Res. 2024;52(D1):D572–D578. https://doi.org/10.1093/nar/gkad897.
Dyken C, Ziegler G, Theobalt C, Seidel HP. High‐speed marching cubes using HistoPyramids. Comput Graph Forum. 2008;27:2028–2039. https://doi.org/10.1111/j.1467-8659.2008.01182.x.
EPAM. Miew, v0.11.1. 2025 https://lifescience.opensource.epam.com/miew/.
Filion D, McNaughton R. Effects & techniques. ACM SIGGRAPH 2008 games. New York, USA: ACM, pp. 133–164. 2008 https://doi.org/10.1145/1404435.1404441.
Fleming J, Magana P, Nair S, Tsenkov M, Bertoni D, Pidruchna I, et al. AlphaFold protein structure database and 3D‐beacons: new data and capabilities. J Mol Biol. 2025;437(15):168967. https://doi.org/10.1016/j.jmb.2025.168967.
Flick J. Depth of Field. 2018 https://catlikecoding.com/unity/tutorials/advanced-rendering/depth-of-field/.
Goodsell DS. Molecule of the Month: Hydrogenase. 2009 https://doi.org/10.2210/rcsb_pdb/mom_2009_3.
Goodsell DS, Austin L, Olson AJ. Illustrate: software for biomolecular illustration. Structure. 2019;27(11):1716–1720.e1. https://doi.org/10.1016/j.str.2019.08.011.
Greene N, Kass M, Miller G. Hierarchical Z‐buffer visibility. In Proceedings of the 20th annual conference on Computer graphics and interactive techniques (SIGGRAPH 93). Association for Computing Machinery, New York, NY, USA, 231–238. 1993 https://doi.org/10.1145/166117.166147.
Hanson. Jmol: an open‐source Java viewer for chemical structures in 3D. 2025. http://www.jmol.org/.
Iambic. Envision. 2023 https://www.iambic-envision.com/.
iChemLabs. ChemDoodle Web Components, v11.0.0. 2025 https://web.chemdoodle.com/.
Jimenez J, Echevarria JI, Sousa T, Gutierrez D. SMAA: enhanced subpixel morphological antialiasing. Comput Graph Forum. 2012;31:355–364. https://doi.org/10.1111/j.1467-8659.2012.03014.x.
Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ. 3D molecular models of whole HIV‐1 virions generated with cellPACK. Faraday Discuss. 2014;169:23–44. https://doi.org/10.1039/C4FD00017J.
Kakkar P, Rao SK, Maurer M, Mane V. Advancements in Order Independent Transparency: A Survey for Real‐Time Rendering Practitioners. 2025 7th International Conference on Software Engineering and Computer Science (CSECS), Taicang, China, 2025, pp. 1–7. 2025 https://doi.org/10.1109/CSECS64665.2025.11009764.
Karabelas P. Screen space shadows. 2020 https://panoskarabelas.com/posts/screen_space_shadows/.
Khronos. Low‐level 3D graphics API based on OpenGL ES. https://www.khronos.org/webgl/.
Krone M, Stone J, Ertl T, Schulten K. Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. EuroVis—Short Papers, 2012, ISBN 978‐3‐905673‐91‐3. 2012 https://doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071.
Le Muzic M, Autin L, Parulek J, Viola I. cellVIEW: a tool for illustrative and multi‐scale rendering of large biomolecular datasets. Eurographics Workshop. Vis Comput Biomed. 2015;2015:61–70. https://doi.org/10.5555/2853955.2853964.
Lottes T. FXAA. Tech. rep., NVIDIA, 2011. 2, 4. 2011 https://developer.download.nvidia.com/assets/gamedev/files/sdk/11/FXAA_WhitePaper.pdf.
Luebke D, Reddy M, Cohen J, Varshney A, Watson B, Huebner R. Level of detail for 3D graphics. San Francisco: Morgan‐Kaufmann; 2002.
Luwanski K, Hlushchenko V, Popenda M, Zok T, Sarzynska J, Martsich D, et al. RNAspider: a webserver to analyze entanglements in RNA 3D structures. Nucleic Acids Res. 2022;50(W1):W663–W669. https://doi.org/10.1093/nar/gkac218.
Lyons B, Isaac E, Choi NH, Do TP, Domingus J, Iwasa J, et al. The Simularium viewer: an interactive online tool for sharing spatiotemporal biological models. Nat Methods. 2022;19:513–515. https://doi.org/10.1038/s41592-022-01442-1.
Marques SM, Borko S, Vavra O, Dvorsky J, Kohout P, Kabourek P, et al. Caver web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Res. 2025;53(W1):W132–W142. https://doi.org/10.1093/nar/gkaf399.
McGuire M, Bavoil L. Weighted blended order‐independent transparency. JComput Graph Techniq. 2013;2(2):122–141.
Mikkelsen M. Bump mapping unparametrized surfaces on the GPU. J Graph GPU Game Tools. 2010;15(1):49–61. https://doi.org/10.1080/2151237X.2010.10390651.
Rammner B, Ozvoldik K, Krieger E. Model of the presynaptic bouton. 2022 http://download.yasara.org/petworld/presynapse/index.html.
Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics. 2015;31(8):1322–1324. https://doi.org/10.1093/bioinformatics/btu829.
Reuter Lab. PePr2Vis Peripheral Protein Protrusion Visualisation, v1.3. 2022 https://reuter-group.github.io/peprmint/pepr2vis/.
Ritschel T, Grosch T, Seidel HP. Approximating dynamic global illumination in image space. In Proceedings of the 2009 symposium on Interactive 3D graphics and games (I3D 09). Association for Computing Machinery, New York, NY, USA, 75–82. 2009 https://doi.org/10.1145/1507149.1507161.
Rodríguez FJC, Frattini G, Phloi‐Montri S, Meireles FTP, 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. https://doi.org/10.1016/j.jmgm.2024.108932.
Rose A, Sehnal D, Goodsell DS, Autin L. Mesoscale explorer: Visual exploration of large‐scale molecular models. Protein Sci. 2024;33(10):e5177. https://doi.org/10.1002/pro.5177.
Rose AS, Hildebrand PW. NGL viewer: a web application for molecular visualization. Nucleic Acids Res. 2015;43(W1):W576–W579. https://doi.org/10.1093/nar/gkv402.
Sehnal D, Bittrich S, Deshpande M, Svobodova 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. https://doi.org/10.1093/nar/gkab314.
Sehnal D, Deshpande M, Varekova RS, Mir S, Berka K, Midlik A, et al. LiteMol suite: interactive web‐based visualization of large‐scale macromolecular structure data. Nat Methods. 2017;14:1121–1122. https://doi.org/10.1038/nmeth.4499.
Sigg C, Weyrich T, Botsch M, Gross M. GPU‐based ray‐casting of quadratic surfaces. The Eurographics Association, 2006, ISSN 1811‐7813. 2006 https://doi.org/10.2312/SPBG/SPBG06/059‐065.
Slaninakova T, Charlop‐Powers Z, Doshchenko V, Rose AS, Midlik A, Sekuła A, et al. MolViewStories: Interactive Molecular Storytelling. 2025 https://molstar.org/mol-view-stories/.
Tarini M, Cignoni P, Montani C. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans vis Comput Graph. 2006;12(5):1237–1244. https://doi.org/10.1109/TVCG.2006.115.
TC39. Specifying JavaScript. https://tc39.es/.
Terrell R. Speck. 2015 https://wwwtyro.github.io/speck/.
Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, et al. iCn3D, a web‐based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. Bioinformatics. 2020;36(1):131–135. https://doi.org/10.1093/bioinformatics/btz502.
Wilhelm BG, Mandad S, Truckenbrodt S, Kröhnert K, Schäfer C, Rammner B, et al. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Science. 2014;344:1023–1028. https://doi.org/10.1126/science.1252884.
Autin L, Barbaro BA, Jewett AI, Ekman A, Verma S, Olson AJ, et al. Integrative structural modelling and visualisation of a cellular organelle. QRB Discov. 2022;3:e11. https://doi.org/10.1017/qrd.2022.10.
Bavoil L, Myers K. Order independent transparency with dual depth peeling. NVIDIA OpenGL SDK. 2008;10(12):2–4. https://developer.download.nvidia.com/SDK/10/opengl/src/dual_depth_peeling/doc/DualDepthPeeling.pdf.
Bekker GJ, Nakamura H, Kinjo AR. Molmil: a molecular viewer for the PDB and beyond. J Chem. 2016;8:42. https://doi.org/10.1186/s13321-016-0155-1.
Beliu G, Altrichter S, Guixà‐González R, Hemberger M, Brauer I, Dahse AK, et al. Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain. Mol Cell. 2021;81(5):905–921.E5. https://doi.org/10.1016/j.molcel.2020.12.042.
Černý J, Malý M, Božíková P, Prchalová T, Svoboda J, Biedermannová L, et al. DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis. Nucleic Acids Res. 2026;54(1):gkaf1491. https://doi.org/10.1093/nar/gkaf1491.
Dobson L, Gerdán C, Tusnády S, Szekeres L, Kuffa K, Langó T, et al. UniTmp: unified resources for transmembrane proteins. Nucleic Acids Res. 2024;52(D1):D572–D578. https://doi.org/10.1093/nar/gkad897.
Dyken C, Ziegler G, Theobalt C, Seidel HP. High‐speed marching cubes using HistoPyramids. Comput Graph Forum. 2008;27:2028–2039. https://doi.org/10.1111/j.1467-8659.2008.01182.x.
EPAM. Miew, v0.11.1. 2025 https://lifescience.opensource.epam.com/miew/.
Filion D, McNaughton R. Effects & techniques. ACM SIGGRAPH 2008 games. New York, USA: ACM, pp. 133–164. 2008 https://doi.org/10.1145/1404435.1404441.
Fleming J, Magana P, Nair S, Tsenkov M, Bertoni D, Pidruchna I, et al. AlphaFold protein structure database and 3D‐beacons: new data and capabilities. J Mol Biol. 2025;437(15):168967. https://doi.org/10.1016/j.jmb.2025.168967.
Flick J. Depth of Field. 2018 https://catlikecoding.com/unity/tutorials/advanced-rendering/depth-of-field/.
Goodsell DS. Molecule of the Month: Hydrogenase. 2009 https://doi.org/10.2210/rcsb_pdb/mom_2009_3.
Goodsell DS, Austin L, Olson AJ. Illustrate: software for biomolecular illustration. Structure. 2019;27(11):1716–1720.e1. https://doi.org/10.1016/j.str.2019.08.011.
Greene N, Kass M, Miller G. Hierarchical Z‐buffer visibility. In Proceedings of the 20th annual conference on Computer graphics and interactive techniques (SIGGRAPH 93). Association for Computing Machinery, New York, NY, USA, 231–238. 1993 https://doi.org/10.1145/166117.166147.
Hanson. Jmol: an open‐source Java viewer for chemical structures in 3D. 2025. http://www.jmol.org/.
Iambic. Envision. 2023 https://www.iambic-envision.com/.
iChemLabs. ChemDoodle Web Components, v11.0.0. 2025 https://web.chemdoodle.com/.
Jimenez J, Echevarria JI, Sousa T, Gutierrez D. SMAA: enhanced subpixel morphological antialiasing. Comput Graph Forum. 2012;31:355–364. https://doi.org/10.1111/j.1467-8659.2012.03014.x.
Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ. 3D molecular models of whole HIV‐1 virions generated with cellPACK. Faraday Discuss. 2014;169:23–44. https://doi.org/10.1039/C4FD00017J.
Kakkar P, Rao SK, Maurer M, Mane V. Advancements in Order Independent Transparency: A Survey for Real‐Time Rendering Practitioners. 2025 7th International Conference on Software Engineering and Computer Science (CSECS), Taicang, China, 2025, pp. 1–7. 2025 https://doi.org/10.1109/CSECS64665.2025.11009764.
Karabelas P. Screen space shadows. 2020 https://panoskarabelas.com/posts/screen_space_shadows/.
Khronos. Low‐level 3D graphics API based on OpenGL ES. https://www.khronos.org/webgl/.
Krone M, Stone J, Ertl T, Schulten K. Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. EuroVis—Short Papers, 2012, ISBN 978‐3‐905673‐91‐3. 2012 https://doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071.
Le Muzic M, Autin L, Parulek J, Viola I. cellVIEW: a tool for illustrative and multi‐scale rendering of large biomolecular datasets. Eurographics Workshop. Vis Comput Biomed. 2015;2015:61–70. https://doi.org/10.5555/2853955.2853964.
Lottes T. FXAA. Tech. rep., NVIDIA, 2011. 2, 4. 2011 https://developer.download.nvidia.com/assets/gamedev/files/sdk/11/FXAA_WhitePaper.pdf.
Luebke D, Reddy M, Cohen J, Varshney A, Watson B, Huebner R. Level of detail for 3D graphics. San Francisco: Morgan‐Kaufmann; 2002.
Luwanski K, Hlushchenko V, Popenda M, Zok T, Sarzynska J, Martsich D, et al. RNAspider: a webserver to analyze entanglements in RNA 3D structures. Nucleic Acids Res. 2022;50(W1):W663–W669. https://doi.org/10.1093/nar/gkac218.
Lyons B, Isaac E, Choi NH, Do TP, Domingus J, Iwasa J, et al. The Simularium viewer: an interactive online tool for sharing spatiotemporal biological models. Nat Methods. 2022;19:513–515. https://doi.org/10.1038/s41592-022-01442-1.
Marques SM, Borko S, Vavra O, Dvorsky J, Kohout P, Kabourek P, et al. Caver web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Res. 2025;53(W1):W132–W142. https://doi.org/10.1093/nar/gkaf399.
McGuire M, Bavoil L. Weighted blended order‐independent transparency. JComput Graph Techniq. 2013;2(2):122–141.
Mikkelsen M. Bump mapping unparametrized surfaces on the GPU. J Graph GPU Game Tools. 2010;15(1):49–61. https://doi.org/10.1080/2151237X.2010.10390651.
Rammner B, Ozvoldik K, Krieger E. Model of the presynaptic bouton. 2022 http://download.yasara.org/petworld/presynapse/index.html.
Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics. 2015;31(8):1322–1324. https://doi.org/10.1093/bioinformatics/btu829.
Reuter Lab. PePr2Vis Peripheral Protein Protrusion Visualisation, v1.3. 2022 https://reuter-group.github.io/peprmint/pepr2vis/.
Ritschel T, Grosch T, Seidel HP. Approximating dynamic global illumination in image space. In Proceedings of the 2009 symposium on Interactive 3D graphics and games (I3D 09). Association for Computing Machinery, New York, NY, USA, 75–82. 2009 https://doi.org/10.1145/1507149.1507161.
Rodríguez FJC, Frattini G, Phloi‐Montri S, Meireles FTP, 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. https://doi.org/10.1016/j.jmgm.2024.108932.
Rose A, Sehnal D, Goodsell DS, Autin L. Mesoscale explorer: Visual exploration of large‐scale molecular models. Protein Sci. 2024;33(10):e5177. https://doi.org/10.1002/pro.5177.
Rose AS, Hildebrand PW. NGL viewer: a web application for molecular visualization. Nucleic Acids Res. 2015;43(W1):W576–W579. https://doi.org/10.1093/nar/gkv402.
Sehnal D, Bittrich S, Deshpande M, Svobodova 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. https://doi.org/10.1093/nar/gkab314.
Sehnal D, Deshpande M, Varekova RS, Mir S, Berka K, Midlik A, et al. LiteMol suite: interactive web‐based visualization of large‐scale macromolecular structure data. Nat Methods. 2017;14:1121–1122. https://doi.org/10.1038/nmeth.4499.
Sigg C, Weyrich T, Botsch M, Gross M. GPU‐based ray‐casting of quadratic surfaces. The Eurographics Association, 2006, ISSN 1811‐7813. 2006 https://doi.org/10.2312/SPBG/SPBG06/059‐065.
Slaninakova T, Charlop‐Powers Z, Doshchenko V, Rose AS, Midlik A, Sekuła A, et al. MolViewStories: Interactive Molecular Storytelling. 2025 https://molstar.org/mol-view-stories/.
Tarini M, Cignoni P, Montani C. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans vis Comput Graph. 2006;12(5):1237–1244. https://doi.org/10.1109/TVCG.2006.115.
TC39. Specifying JavaScript. https://tc39.es/.
Terrell R. Speck. 2015 https://wwwtyro.github.io/speck/.
Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, et al. iCn3D, a web‐based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. Bioinformatics. 2020;36(1):131–135. https://doi.org/10.1093/bioinformatics/btz502.
Wilhelm BG, Mandad S, Truckenbrodt S, Kröhnert K, Schäfer C, Rammner B, et al. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Science. 2014;344:1023–1028. https://doi.org/10.1126/science.1252884.
Grant Information:
DBI-2321666 National Science Foundation; DE-SC0019749 U.S. Department of Energy; 5U54AI170855 United States NH NIH HHS; GM120604 United States NH NIH HHS; R01GM157729 United States NH NIH HHS; 22-30571M Grantová Agentura České Republiky
Contributed Indexing:
Keywords: GPU accelerated; global illumination; immersive AR/VR; mesoscale molecular models; web molecular graphics
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20260313 Date Completed: 20260313 Latest Revision: 20260313
Update Code:
20260313
DOI:
10.1002/pro.70514
PMID:
41820803
Database:
MEDLINE
Weitere Informationen
Web-based molecular graphics have transformed the interactive visualization of molecular data, leveraging modern web technologies that provide GPU acceleration, optimized JavaScript engines, and seamless access across devices without additional software installation. We present the graphics engine at the core of the Mol* toolkit, a high-performance, open-source framework that is widely adopted in academia and industry, including by the Protein Data Bank, UniProt, EMDB, and AlphaFold DB. The engine combines a comprehensive styling system with a suite of optimized rendering primitives, including real-time surface generation, to deliver both flexibility and visual fidelity. Efficient handling of large-scale molecular scenes is achieved through level-of-detail management, GPU instancing, spatial acceleration structures, and frustum/occlusion culling. A screen-space global illumination model provides scalable, high-quality lighting, while integrated AR/VR support enables immersive molecular exploration. Together, these capabilities enable engaging, real-time, high-fidelity visualization of molecular systems, across a wide range of scales, from single atoms to billion-atom mesoscale assemblies, demonstrating the strengths of a bespoke web-native rendering engine for molecular graphics, available at https://molstar.org.
(© 2026 The Protein Society.)