Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model
VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics engine utilizing impostor-based techniques and adaptive level...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1588661/full |
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| author | Maxime Maria Valentin Guillaume Simon Guionnière Nicolas Dacquay Cyprien Plateau–Holleville Vincent Larroque Vincent Larroque Jean Lardé Jean Lardé Yassine Naimi Jean-Philip Piquemal Jean-Philip Piquemal Jean-Philip Piquemal Guillaume Levieux Nathalie Lagarde Stéphane Mérillou Matthieu Montes Matthieu Montes |
| author_facet | Maxime Maria Valentin Guillaume Simon Guionnière Nicolas Dacquay Cyprien Plateau–Holleville Vincent Larroque Vincent Larroque Jean Lardé Jean Lardé Yassine Naimi Jean-Philip Piquemal Jean-Philip Piquemal Jean-Philip Piquemal Guillaume Levieux Nathalie Lagarde Stéphane Mérillou Matthieu Montes Matthieu Montes |
| author_sort | Maxime Maria |
| collection | DOAJ |
| description | VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics engine utilizing impostor-based techniques and adaptive level-of-detail (LOD) rendering. This approach significantly reduces memory usage and enables real-time visualization and manipulation of large molecular systems. Performance benchmarks against VMD, PyMOL, and ChimeraX using a 114-million-bead Martini minimal whole-cell model demonstrate VTX’s efficiency, maintaining consistent frame rates even under interactive manipulation on standard computer hardware. VTX incorporates features such as Screen-Space Ambient Occlusion (SSAO) for enhanced depth perception and free-fly navigation for intuitive exploration of large molecular systems. VTX is open-source and free for non commercial use. Binaries for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. VTX source code is available at https://github.com/VTX-Molecular-Visualization. |
| format | Article |
| id | doaj-art-385b46062d324c4f9e5f7d82c9f039c2 |
| institution | OA Journals |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-385b46062d324c4f9e5f7d82c9f039c22025-08-20T02:32:33ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-06-01510.3389/fbinf.2025.15886611588661Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell modelMaxime Maria0Valentin Guillaume1Simon Guionnière2Nicolas Dacquay3Cyprien Plateau–Holleville4Vincent Larroque5Vincent Larroque6Jean Lardé7Jean Lardé8Yassine Naimi9Jean-Philip Piquemal10Jean-Philip Piquemal11Jean-Philip Piquemal12Guillaume Levieux13Nathalie Lagarde14Stéphane Mérillou15Matthieu Montes16Matthieu Montes17XLIM, UMR CNRS 7252, Université de Limoges, Limoges, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceXLIM, UMR CNRS 7252, Université de Limoges, Limoges, FranceXLIM, UMR CNRS 7252, Université de Limoges, Limoges, FranceQubit Pharmaceuticals SAS, Paris, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceQubit Pharmaceuticals SAS, Paris, FranceQubit Pharmaceuticals SAS, Paris, FranceLCT, UMR 7616 CNRS, Sorbonne Université, Paris, FranceDepartment of Biomedical Engineering, University of Texas at Austin, Austin, TX, United StatesInstitut Universitaire de France, Paris, FranceLaboratoire CEDRIC, EA 4626, Conservatoire National des Arts et Métiers, Paris, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceXLIM, UMR CNRS 7252, Université de Limoges, Limoges, FranceLaboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, FranceInstitut Universitaire de France, Paris, FranceVTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics engine utilizing impostor-based techniques and adaptive level-of-detail (LOD) rendering. This approach significantly reduces memory usage and enables real-time visualization and manipulation of large molecular systems. Performance benchmarks against VMD, PyMOL, and ChimeraX using a 114-million-bead Martini minimal whole-cell model demonstrate VTX’s efficiency, maintaining consistent frame rates even under interactive manipulation on standard computer hardware. VTX incorporates features such as Screen-Space Ambient Occlusion (SSAO) for enhanced depth perception and free-fly navigation for intuitive exploration of large molecular systems. VTX is open-source and free for non commercial use. Binaries for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. VTX source code is available at https://github.com/VTX-Molecular-Visualization.https://www.frontiersin.org/articles/10.3389/fbinf.2025.1588661/fullmolecular visualizationmolecular graphicsusabilitymolecular modelingmolecular dynamicshigh-performance computing |
| spellingShingle | Maxime Maria Valentin Guillaume Simon Guionnière Nicolas Dacquay Cyprien Plateau–Holleville Vincent Larroque Vincent Larroque Jean Lardé Jean Lardé Yassine Naimi Jean-Philip Piquemal Jean-Philip Piquemal Jean-Philip Piquemal Guillaume Levieux Nathalie Lagarde Stéphane Mérillou Matthieu Montes Matthieu Montes Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model Frontiers in Bioinformatics molecular visualization molecular graphics usability molecular modeling molecular dynamics high-performance computing |
| title | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model |
| title_full | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model |
| title_fullStr | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model |
| title_full_unstemmed | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model |
| title_short | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model |
| title_sort | interactive visualization of large molecular systems with vtx example with a minimal whole cell model |
| topic | molecular visualization molecular graphics usability molecular modeling molecular dynamics high-performance computing |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1588661/full |
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