Overview and applications of map and model validation tools in the CCP-EM software suite.
Overview and applications of map and model validation tools in the CCP-EM software suite.
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DOI：
10.1039/d2fd00103a
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发表时间：
2022-11-08
影响因子：
3.4
通讯作者：
Winn, Martyn D.
中科院分区：
文献类型：
--
作者：
Joseph, Agnel Praveen;Malhotra, Sony;Burnley, Tom;Winn, Martyn D.
低温电子显微镜(CRYO-EM)是近年来发展起来的一种研究大分子结构的有力手段。尽管可实现的最佳分辨率正在提高，但大部分数据的分辨率仍然低于3？，在这种情况下，建立或拟合原子模型并不是一件容易的事情。从地图得到的地图重建和原子模型也容易在数据处理的不同阶段积累误差。在这里，我们强调需要评估模型几何图形和适应不同分辨率的数据。对SARS-CoV-2低温EM结构的评估突出了与数据相一致的偏向，即优化模型几何以与最常见的构象相一致。我们提出了Coval Web服务，它提供了多种验证度量来反映从SARS-CoV-2结构的冷冻-EM数据派生的原子模型的质量。我们证明，进一步的改进可以在不损失几何质量的情况下改善与数据的一致性。我们还讨论了旨在解决当前一些缺点的CCP-EM最近的事态发展。来自Cryo-EM的原子模型显示出对几何质量的偏好，但代价是与地图数据的一致性。这项研究突出了缺乏验证标准和CCP-EM在这方面的努力和相关发展。
Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings. Atomic models from cryo-EM show a preference for geometric quality with the expense of agreement with the map data. This study highlights the lack of validation standards and CCP-EM efforts and related developments in this context.
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DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
DOI：
10.1016/j.ymeth.2016.03.007
发表时间：
2016-05-01
期刊：
Methods (San Diego, Calif.)
影响因子：
--
作者：
Joseph AP;Malhotra S;Burnley T;Wood C;Clare DK;Winn M;Topf M
通讯作者：
Topf M
影响因子：
5.7
作者：
Herzik, Mark A., Jr.;Fraser, James S.;Lander, Gabriel C.
通讯作者：
Lander, Gabriel C.
影响因子：
14.9
作者：
Drozdetskiy A;Cole C;Procter J;Barton GJ
通讯作者：
Barton GJ