Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia.
Bioinformatics. 2020 Apr 1;36(7):2237-2243. doi: 10.1093/bioinformatics/btz904.
No rigorous statistical tests for detecting point-group symmetry in three-dimensional (3D) charge density maps obtained by electron microscopy (EM) and related techniques have been developed.
We propose a method for determining the point-group symmetry of 3D charge density maps obtained by EM and related techniques. Our ab initio algorithm does not depend on atomic coordinates but utilizes the density map directly. We validate the approach for a range of publicly available single-particle cryo-EM datasets. In straightforward cases, our method enables fully automated single-particle 3D reconstruction without having to input an arbitrarily selected point-group symmetry. When pseudo-symmetry is present, our method provides statistics quantifying the degree to which the 3D density agrees with the different point-groups tested.
The software is freely available at https://github.com/hael/SIMPLE3.0.
目前还没有针对电子显微镜（EM）和相关技术获得的三维（3D）电荷密度图中点群对称性的严格统计检验方法。
我们提出了一种用于确定通过 EM 和相关技术获得的 3D 电荷密度图中点群对称性的方法。我们的从头算法不依赖于原子坐标，而是直接利用密度图。我们针对一系列公开可用的单颗粒冷冻电镜数据集验证了该方法。在简单的情况下，我们的方法可以实现全自动的单颗粒 3D 重建，而无需输入任意选择的点群对称性。当存在拟对称性时，我们的方法提供了量化 3D 密度与所测试的不同点群相符程度的统计信息。
该软件可在 https://github.com/hael/SIMPLE3.0 上免费获得。
