Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jun 6:5:1588661.
doi: 10.3389/fbinf.2025.1588661. eCollection 2025.

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

Maxime Maria  1 , Valentin Guillaume  2 , Simon Guionnière  2 , Nicolas Dacquay  2 , Cyprien Plateau-Holleville  1 , Vincent Larroque  1   3 , Jean Lardé  2   3 , Yassine Naimi  3 , Jean-Philip Piquemal  4   5   6 , Guillaume Levieux  7 , Nathalie Lagarde  2 , Stéphane Mérillou  1 , Matthieu Montes  2   6
Affiliations

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

Maxime Maria et al. Front Bioinform. .

Abstract

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.

Keywords: high-performance computing; molecular dynamics; molecular graphics; molecular modeling; molecular visualization; protein structure; structural biology; usability.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

FIGURE 1
FIGURE 1
Illustration of the complexity of mesh-based and impostor-based sphere representations. (a) Mesh-based spheres with increasing triangle counts (80, 320, 720, and 1,280 respectively) generated with Blender; (b) VTX’s impostor-based sphere (with only one vertex).
FIGURE 2
FIGURE 2
Impact of the intensity of the Screen‐Space Ambient Occlusion (SSAO) on a close-up rendering of a large molecular system (Stevens et al., 2023): (a) No SSAO; (b) Low intensity SSAO; (c) High intensity SSAO.
FIGURE 3
FIGURE 3
Wide-system view of the lipids, membrane proteins, and ribosomes (36,566,468 Martini beads) of the 2023 Martini minimal whole cell model rendered in real-time with VMD (a) on the left, and VTX (b) on the right. These illustrations were captured on a Dell precision 5480 laptop equipped with an Intel i7-13800H, 32 GB of RAM and a NVidia Quadro RTX 3000 GPU. All attempts to improve the rendering with VMD on this setup resulted in a freeze of the application.
See this image and copyright information in PMC

References

    1. Abraham M., Alekseenko A., Basov V., Bergh C., Briand E., Brown A., et al. (2024). GROMACS 2024.0 Manual.
    1. Amaro R. E., Åqvist J., Bahar I., Battistini F., Bellaiche A., Beltran D., et al. (2025). The need to implement FAIR principles in biomolecular simulations. Nat. Methods 22, 641–645. 10.1038/s41592-025-02635-0 - DOI - PubMed
    1. Bagur P. D., Shivashankar N., Natarajan V. (2012). “Improved quadric surface impostors for large bio-molecular visualization,” in Proceedings of the eighth Indian conference on computer vision, graphics and image processing, ICVGIP ’12 (New York, NY, USA: Association for Computing Machinery; ).
    1. Coshic K., Maffeo C., Winogradoff D., Aksimentiev A. (2024). The structure and physical properties of a packaged bacteriophage particle. Nature 627, 905–914. 10.1038/s41586-024-07150-4 - DOI - PMC - PubMed
    1. Gilbert B. R., Thornburg Z. R., Brier T. A., Stevens J. A., Grünewald F., Stone J. E., et al. (2023). Dynamics of chromosome organization in a minimal bacterial cell. Front. Cell Dev. Biol. 11 - 2023. 10.3389/fcell.2023.1214962 - DOI - PMC - PubMed

LinkOut - more resources