Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Structure Pub Date : 2024-07-29 DOI:10.1016/j.str.2024.07.003

引用次数: 0

Abstract

With the advent of modern technologies for cryo-electron tomography (cryo-ET), high-quality tilt series are more rapidly acquired than processed and analyzed. Thus, a robust and fast-automated alignment for batch processing in cryo-ET is needed. While different software packages have made available several approaches for automated marker-based alignment of tilt series, manual user intervention remains necessary for many datasets, thus preventing high-throughput tomography.

We have developed a MATLAB-based framework integrated into the Dynamo software package for automatic detection of fiducial markers that generates a robust alignment model with minimal input parameters. This approach allows high-throughput, unsupervised volume reconstruction. This new module extends Dynamo with a large repertory of tools for tomographic alignment and reconstruction, as well as specific visualization browsers to rapidly assess the biological relevance of the dataset. Our approach has been successfully tested on a broad range of datasets that include diverse biological samples and cryo-ET modalities.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

在 Dynamo 中基于靶标自动对准低温电子断层扫描倾斜序列

随着现代低温电子断层扫描（cryo-ET）技术的出现，高质量倾斜序列的获取比处理和分析更加迅速。因此，在低温电子断层扫描中需要一种用于批量处理的强大而快速的自动配准方法。我们开发了一个基于 MATLAB 的框架，集成到 Dynamo 软件包中，用于自动检测靶标，以最小的输入参数生成稳健的配准模型。这种方法可实现高通量、无监督的容积重建。这个新模块扩展了 Dynamo，为断层配准和重建提供了大量工具，还提供了特定的可视化浏览器，以快速评估数据集的生物学相关性。我们的方法已在广泛的数据集上进行了成功测试，这些数据集包括不同的生物样本和低温电子显微镜模式。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Structure 生物-生化与分子生物学

CiteScore

8.90

自引率

1.80%

发文量

155

审稿时长

3-8 weeks

期刊介绍： Structure aims to publish papers of exceptional interest in the field of structural biology. The journal strives to be essential reading for structural biologists, as well as biologists and biochemists that are interested in macromolecular structure and function. Structure strongly encourages the submission of manuscripts that present structural and molecular insights into biological function and mechanism. Other reports that address fundamental questions in structural biology, such as structure-based examinations of protein evolution, folding, and/or design, will also be considered. We will consider the application of any method, experimental or computational, at high or low resolution, to conduct structural investigations, as long as the method is appropriate for the biological, functional, and mechanistic question(s) being addressed. Likewise, reports describing single-molecule analysis of biological mechanisms are welcome. In general, the editors encourage submission of experimental structural studies that are enriched by an analysis of structure-activity relationships and will not consider studies that solely report structural information unless the structure or analysis is of exceptional and broad interest. Studies reporting only homology models, de novo models, or molecular dynamics simulations are also discouraged unless the models are informed by or validated by novel experimental data; rationalization of a large body of existing experimental evidence and making testable predictions based on a model or simulation is often not considered sufficient.