Department of Computer and Information Science, University of Konstanz, Konstanz 76484, Germany.
Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia.
Bioinformatics. 2023 Feb 3;39(2). doi: 10.1093/bioinformatics/btad083.
Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics and processes, visual analytics can help to interpret MD simulation data. APL@Voro is a software for the interactive visualization and analysis of cell membrane simulations. Here, we present the new APL@Voro, which has been continuously developed since its initial release in 2013. We discuss newly implemented algorithms, methodologies and features, such as the interactive comparison of related simulations and methods to assign lipids to either the upper or lower leaflet.
The current open-source version of APL@Voro can be downloaded from http://aplvoro.com.
细胞膜的分子动力学 (MD) 模拟可以更好地理解复杂过程，例如改变膜动力学、脂筏以及大分子进入/穿过细胞膜的过程。为了探索和理解细胞膜的组成、动力学和过程，可视化分析有助于解释 MD 模拟数据。APL@Voro 是一款用于交互式可视化和分析细胞膜模拟的软件。在这里，我们介绍了自 2013 年首次发布以来不断发展的新版本 APL@Voro。我们讨论了新实现的算法、方法和功能，例如相关模拟的交互式比较，以及将脂质分配到上或下叶的方法。
可以从 http://aplvoro.com 下载当前的开源版本的 APL@Voro。
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