Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography.
Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography.
复制标题
评估评分函数，以对来自冷冻电子断层扫描的3D亚断层图像簇的质量进行排名。
DOI：
10.1016/j.jsb.2021.107727
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发表时间：
2021-06
影响因子：
3
通讯作者：
Alber F
中科院分区：
文献类型：
--
作者：
Singla J;White KL;Stevens RC;Alber F
冷冻电子断层扫描提供了机会，在原位内源性复合物的无监督发现。这个过程通常需要粒子拾取、聚类和子断层图的对齐，以产生复合物的平均结构。当应用于异质样品时，无模板聚类和子断层图的对齐可能会导致发现未知内源性复合物的结构。然而，此类方法需要评分函数来测量并准确地对对齐的子断层图像集群的质量进行排名，而这可能会受到错误分类的复合体和对齐错误的污染的影响。在这里，我们提供了第一项研究，以评估超过15个评分函数的有效性，用于评估subtomography集群的质量，不同的结构错位和污染的数量，由于错误分类的复合物。我们评估了实验和模拟subtomographs地面实况数据集。我们的分析表明，评分函数的鲁棒性差异很大。大多数分数是敏感的subtomographs的信噪比，往往需要高斯滤波作为预处理，以提高性能。两个评分函数，光谱信噪比为基础的傅立叶壳相关和皮尔逊相关在傅立叶域与丢失的楔形校正，显示了强大的排名subtomogram集群没有任何预处理，无论SNR水平的subtomogram。在这两个评分函数中，基于光谱SNR的傅立叶壳相关计算速度最快，是处理大量子断层图像的更好选择。我们的研究结果提供了一个指导，选择一个准确的评分功能的无模板的方法来检测复杂的异质性样品。
Cryo-electron tomography provides the opportunity for unsupervised discovery of endogenous complexes in situ. This process usually requires particle picking, clustering and alignment of subtomograms to produce an average structure of the complex. When applied to heterogeneous samples, template-free clustering and alignment of subtomograms can potentially lead to the discovery of structures for unknown endogenous complexes. However, such methods require scoring functions to measure and accurately rank the quality of aligned subtomogram clusters, which can be compromised by contaminations from misclassified complexes and alignment errors. Here, we provide the first study to assess the effectiveness of more than 15 scoring functions for evaluating the quality of subtomogram clusters, which differ in the amount of structural misalignments and contaminations due to misclassified complexes. We assessed both experimental and simulated subtomograms as ground truth data sets. Our analysis showed that the robustness of scoring functions varies largely. Most scores were sensitive to the signal-to-noise ratio of subtomograms and often required Gaussian filtering as preprocessing for improved performance. Two scoring functions, Spectral SNR-based Fourier Shell Correlation and Pearson Correlation in the Fourier domain with missing wedge correction, showed a robust ranking of subtomogram clusters without any preprocessing and irrespective of SNR levels of subtomograms. Of these two scoring functions, Spectral SNR-based Fourier Shell Correlation was fastest to compute and is a better choice for handling large numbers of subtomograms. Our results provide a guidance for choosing an accurate scoring function for template-free approaches to detect complexes from heterogeneous samples.
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影响因子：
48
作者：
Beck, Martin;Malmstroem, Johan A.;Lange, Vinzenz;Schmidt, Alexander;Deutsch, Eric W.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
DOI：
10.1093/bioinformatics/btr207
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Xu M;Beck M;Alber F
通讯作者：
Alber F
影响因子：
5.7
作者：
Scheres, Sjors H. W.;Melero, Roberto;Carazo, Jose-Maria
通讯作者：
Carazo, Jose-Maria
影响因子：
8
作者：
Studholme, C;Hill, DLG;Hawkes, DJ
通讯作者：
Hawkes, DJ
影响因子：
3
作者：
Shatsky, Maxim;Hall, Richard J.;Brenner, Steven E.;Glaeser, Robert M.
通讯作者：
Glaeser, Robert M.