STOPGAP, an open-source package for template matching, subtomogram alignment, and classification.
STOPGAP, an open-source package for template matching, subtomogram alignment, and classification.
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STOPGAP，一个用于模板匹配、断层扫描对齐和分类的开源包。
DOI：
10.1101/2023.12.20.572665
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Wagner,Jonathan
中科院分区：
文献类型：
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作者：
Wan,William;Khavnekar,Sagar;Wagner,Jonathan
冷冻电子断层扫描（cryo-ET）能够对复杂的生物样本（如病毒颗粒、细胞切片，在某些情况下甚至是整个细胞）进行分子分辨率的3D成像。这使得分子在其近天然环境中的结构表征成为可能，而无需纯化或分离，从而保留生物信息，例如不同分子种类之间的构象状态和空间关系。亚断层图像平均是一种图像处理工作流程，允许用户利用冷冻ET数据来识别和定位目标分子，确定重复分子种类的高分辨率结构并对不同的构象状态进行分类。在这里，描述了STOPGAP，这是一个用于断层图像平均的开源软件包，旨在为用户提供对这些步骤的精细控制。在提供详细描述的图像处理算法，STOPGAP使用，这份手稿也旨在作为一个技术资源，以用户以及进一步的社区驱动的软件开发。
Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image-processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species and classify different conformational states. Here, STOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of these steps, is described. In providing detailed descriptions of the image-processing algorithms that STOPGAP uses, this manuscript is also intended to serve as a technical resource to users as well as for further community-driven software development.