Cryo_fit：用于 cryo-EM 的灵活适配的民主化。
Cryo_fit: Democratization of flexible fitting for cryo-EM.
机构信息
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, USA.
出版信息
J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.
Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.
低温电子显微镜（cryo-EM）技术正在成为一种描述生物分子复合物在高分辨率下天然构象的首选方法。近年来，cryo-EM 的快速发展对硬件和软件都提出了对自动化解决方案的高需求。通过分子动力学（MD）模拟对原子模型进行灵活拟合三维（3D）cryo-EM 重构是一种流行的技术，但通常需要计算机模拟方面的技术专长。本工作介绍了 cryo_fit，这是一个使用 MD 模拟自动将原子模型拟合到 cryo-EM 图谱中的软件包。该软件包与 Phenix 软件套件集成。该模块旨在以可重复的方式自动完成 MD 模拟的多个步骤，并通过 Phenix 来促进精修和验证。通过使用 cryo_fit，即使是对 MD 模拟经验很少的科学家也可以自动生成高质量的原子模型，并更好地利用 cryo-EM 的潜力。
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