使用VTX对大分子系统进行交互式可视化：以最小全细胞模型为例。

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

作者信息

Maria Maxime, Guillaume Valentin, Guionnière Simon, Dacquay Nicolas, Plateau-Holleville Cyprien, Larroque Vincent, Lardé Jean, Naimi Yassine, Piquemal Jean-Philip, Levieux Guillaume, Lagarde Nathalie, Mérillou Stéphane, Montes Matthieu

机构信息

XLIM, UMR CNRS 7252, Université de Limoges, Limoges, France.

Laboratoire GBCM, EA 7528, Conservatoire National des Artset Métiers, Paris, France.

出版信息

Front Bioinform. 2025 Jun 6;5:1588661. doi: 10.3389/fbinf.2025.1588661. eCollection 2025.

DOI:10.3389/fbinf.2025.1588661

PMID:40546732

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12179134/

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.

摘要

VTX是一款开源分子可视化软件，旨在克服现有实时分子可视化软件在处理大量分子数据集时的缩放限制。VTX采用了一种无网格分子图形引擎，利用基于 impostor 的技术和自适应细节层次（LOD）渲染。这种方法显著减少了内存使用，并能够对大型分子系统进行实时可视化和操作。使用包含1.14亿个珠子的马提尼最小全细胞模型对VMD、PyMOL和ChimeraX进行性能基准测试，结果表明VTX具有高效性，即使在标准计算机硬件上进行交互式操作时也能保持一致的帧率。VTX还集成了诸如屏幕空间环境光遮蔽（SSAO）等功能，以增强深度感知，并提供自由飞行导航功能，以便直观地探索大型分子系统。VTX是开源的，非商业用途免费。可从http://vtx.drugdesign.fr获取适用于Windows和Ubuntu Linux的二进制文件。VTX的源代码可从https://github.com/VTX-Molecular-Visualization获取。