New tools for the analysis and validation of cryo-EM maps and atomic models.
New tools for the analysis and validation of cryo-EM maps and atomic models.
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DOI：
10.1107/s2059798318009324
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发表时间：
2018-09-01
期刊：
影响因子：
--
通讯作者：
Urzhumtsev A
中科院分区：
文献类型：
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作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
新的方法和PHENIX工具的质量评估cryo-EM地图，原子模型和模型到地图拟合。这些工具的高分辨率cryo-EM地图和相应的原子模型的系统应用的结果进行了分析和讨论。电子低温显微镜（cryo-EM）领域的最新进展导致了生物大分子原子模型数量的迅速增加，这些模型已经使用这种技术解决并保存在蛋白质数据库和电子显微镜数据库中。与大分子晶体学类似，需要这些模型和图谱的验证工具。虽然这些验证工具中的一些可以从晶体学中借用，但需要专门为冷冻EM验证设计的新方法。在这里，新的计算方法和工具，在PHENIX中实现的讨论，包括d 99估计分辨率，phenix.auto_sharpen，以改善地图和phenix.mtriage分析cryo-EM地图。有人建议，cryo-EM半图和掩模应存放，以方便评估和验证cryo-EM衍生的原子模型和地图。这些工具的应用，沉积的冷冻EM原子模型和地图。
New methods and PHENIX tools for quality assessment of cryo-EM maps, atomic models and model-to-map fitting are presented. Results of systematic application of these tools to high-resolution cryo-EM maps and corresponding atomic models are analyzed and discussed. Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d 99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.