PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis
PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis
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DOI：
10.1016/j.jsb.2011.12.003
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发表时间：
2012-05-01
影响因子：
3
通讯作者：
Foerster, Friedrich
中科院分区：
文献类型：
--
作者：
Hrabe, Thomas;Chen, Yuxiang;Foerster, Friedrich
冷冻电子断层扫描（CET）是一种用于在接近天然条件下研究大分子结构的三维成像技术。对断层图像中描绘的大分子群体进行深入分析需要识别与推定颗粒对应的子断层图像，对子断层图像进行平均以增强其信号，并进行分类以捕获它们之间的结构变化。在这里，我们介绍了开源平台PyTom，它在Python工具箱中统一了标准的断层图像处理步骤。对于子断层图像平均，我们实现了自适应调整的评分和采样，明显提高了平均值的分辨率相比，静态策略。此外，我们提出了一种新的随机分类方法，产生更准确的分类结果比两个确定性的方法在模拟。我们证明，PyTom工作流程分别为核糖体和GroEL（14）/GroEL（4）GroES（7）的模拟和实验子断层图的比对和分类以及酵母细胞裂解物中核糖体605亚基的分析产生了可靠的结果。PyTom可以并行处理大量的断层图像，但也为算法开发提供了一个方便、可持续的环境。(C)2011 Elsevier Inc. All rights reserved.
Cryo-electron tomography (CET) is a three-dimensional imaging technique for structural studies of macromolecules under close-to-native conditions. In-depth analysis of macromolecule populations depicted in tomograms requires identification of subtomograms corresponding to putative particles, averaging of subtomograms to enhance their signal, and classification to capture the structural variations among them. Here, we introduce the open-source platform PyTom that unifies standard tomogram processing steps in a python toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies. Furthermore, we present a novel stochastic classification method that yields significantly more accurate classification results than two deterministic approaches in simulations. We demonstrate that the PyTom workflow yields faithful results for alignment and classification of simulated and experimental subtomograms of ribosomes and GroEL(14)/GroEL(4)GroES(7), respectively, as well as for the analysis of ribosomal 605 subunits in yeast cell lysate. PyTom enables parallelized processing of large numbers of tomograms, but also provides a convenient, sustainable environment for algorithmic development. (C) 2011 Elsevier Inc. All rights reserved.