Frontiers in Bioinformatics (Jun 2025)

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

  • 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

DOI
https://doi.org/10.3389/fbinf.2025.1588661
Journal volume & issue
Vol. 5

Abstract

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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.

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