BRIEF RESEARCH REPORT article

Front. Bioinform.

Sec. Data Visualization

Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1588661

This article is part of the Research Topic14th International Meeting on Visualizing Biological Data (VIZBI 2024)View all 3 articles

INTERACTIVE VISUALIZATION OF LARGE MOLECULAR SYSTEMS WITH VTX: EXAMPLE WITH A MINIMAL WHOLE-CELL MODEL *

Provisionally accepted
Maxime MariaMaxime Maria1*Valentin GuillaumeValentin Guillaume2Simon GuionnièreSimon Guionnière2Dacquay NicolasDacquay Nicolas2Cyprien Plateau-HollevilleCyprien Plateau-Holleville1Vincent LarroqueVincent Larroque1Jean LardeJean Larde2Yassine NaimiYassine Naimi3Jean-Philip PiquemalJean-Philip Piquemal4Guillaume LevieuxGuillaume Levieux5Nathalie LagardeNathalie Lagarde2Stephane MerillouStephane Merillou1Matthieu MontesMatthieu Montes2*
  • 1UMR7252 XLIM, Limoges, Limousin, France
  • 2Conservatoire National des Arts et Métiers (CNAM), Paris, France
  • 3Qubit Pharmaceuticals, Paris, France
  • 4UMR7616 Laboratoire de Chimie Théorique (LCT), Paris, Île-de-France, France
  • 5Centre d'Etudes et De Recherche en Informatique et Communications, Paris, France

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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.

Keywords: molecular visualization, Molecular graphics, usability, Molecular modeling, molecular dynamics, high-performance computing, protein structure, Structural Biology

Received: 06 Mar 2025; Accepted: 19 May 2025.

Copyright: © 2025 Maria, Guillaume, Guionnière, Nicolas, Plateau-Holleville, Larroque, Larde, Naimi, Piquemal, Levieux, Lagarde, Merillou and Montes. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Maxime Maria, UMR7252 XLIM, Limoges, 87060, Limousin, France
Matthieu Montes, Conservatoire National des Arts et Métiers (CNAM), Paris, France

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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