Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.
Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.
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DOI：
10.1371/journal.pcbi.1005897
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发表时间：
2018-03
影响因子：
4.3
通讯作者：
Harris SA
中科院分区：
文献类型：
--
作者：
Solernou A;Hanson BS;Richardson RA;Welch R;Read DJ;Harlen OG;Harris SA
波动有限元分析 (FFEA) 是一个软件包，旨在对蛋白质和其他球状大分子进行连续介质力学模拟。它将传统的有限元方法与随机热噪声相结合，适用于介观尺度（长度尺度在 5 nm 至 1 μm 范围内）的大型蛋白质和蛋白质复合物的模拟，而目前建模工具还很少。它需要 3D 体积信息作为输入，这些信息可以是低分辨率结构信息，例如冷冻电子断层扫描 (cryo-ET) 图，也可以是可以从中提取体积信息的更高分辨率的原子坐标。在本文中，我们介绍了用于执行 FFEA 模拟的开源软件包，该软件包是根据 GPLv3 许可证发布的。该软件包包括 FFEA 的 C++ 实现，以及帮助用户从电子显微镜数据库 (EMDB) 或蛋白质数据库 (PDB) 数据文件设置系统的工具。我们还提供 PyMOL 插件来执行基本可视化，并提供其他 Python 工具来分析 FFEA 模拟轨迹。本手稿提供了 FFEA 方法的基本背景，描述了核心力学模型的实现以及分子间相互作用和溶剂环境如何包含在该框架内。我们为潜在的 FFEA 用户提供了如何参考该包的第一个版本附带的公开在线教程和手册来设置 FFEA 模拟的实用概述。
Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package.
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影响因子：
3.9
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