All-Atom Membrane Builder via Multiscale Simulation,Journal of Chemical Information and Modeling

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All-Atom Membrane Builder via Multiscale Simulation
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2024-09-09 , DOI: 10.1021/acs.jcim.4c01059
Siyoung Kim ₁

Affiliation

I present an automated and flexible tool designed for constructing bilayer membranes at all-atom (AA) resolution. The builder initiates the construction and equilibration of bilayer membranes at Martini coarse-grained (CG) resolution, followed by resolution enhancement to the atomic level using the accompanying backmapping tool. Notably, this tool enables users to create bilayer membranes with user-defined lipid compositions and protein structures, while also offering the flexibility to accommodate new lipid types. To assess the simplicity and robustness of the tool, I demonstrate the construction of several membranes incorporating protein structures. The tool is freely available at github.com/ksy141/mstool.

中文翻译：

通过多尺度模拟的全原子膜构建器

我提出了一种自动化且灵活的工具，旨在以全原子（AA）分辨率构建双层膜。构建器以 Martini 粗粒度 (CG) 分辨率启动双层膜的构建和平衡，然后使用随附的反向映射工具将分辨率增强到原子级别。值得注意的是，该工具使用户能够创建具有用户定义的脂质成分和蛋白质结构的双层膜，同时还提供适应新脂质类型的灵活性。为了评估该工具的简单性和稳健性，我演示了几种包含蛋白质结构的膜的构建。该工具可在 github.com/ksy141/mstool 上免费获取。

更新日期：2024-09-09

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