Low Resolution Refinement of Atomic Models Against Crystallographic Data.
Low Resolution Refinement of Atomic Models Against Crystallographic Data.
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根据晶体学数据对原子模型进行低分辨率细化。
DOI：
10.1007/978-1-4939-7000-1_23
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Nicholls RA
中科院分区：
文献类型：
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作者：
Nicholls RA
本文介绍了在低分辨率加密和地图计算过程中遇到的一些问题。精炼被认为是贝叶斯定理的应用，允许来自各种来源的信息的组合，包括晶体学实验数据和先前的化学和结构知识。与大分子相关的先验知识的来源包括基本的化学信息，如键和角度，来自已知同系物的参考模型的结构信息，关于二级结构的知识，氢键模式，以及分子的非晶体学相关副本的相似性。此外，利用封装局部构象保守的先验信息，保持局部原子间距离与起始原子模型中的距离相似。设计一个准确的似然函数模型参数和观测数据之间的唯一联系的重要性，强调。该评论还再次强调了相位的重要性，并描述了如何使用原始观测振幅可以得到一个更好的计算和“真实”的地图之间的相关性。它示出，非常嘈杂的或不存在的意见，可以取代计算的结构因子，根据原子模型的准确性加权。这种方法有助于使地图平滑。然而，这种替换应该谨慎使用，因为模型中的误差偏差可能太大而无法避免。一般建议，每当计算新的地图时，应通过检查地图中没有原子模型的部分来判断地图质量。还要注意的是，建议使用多个模糊和锐化的贴图，因为晶体的不同部分可能表现出不同程度的移动性。这样做可以允许精确构建原子模型，考虑整体形状以及更精细的结构细节。本综述中描述的一些结果已在REFMAC 5、ProSMART和LORESTR程序中实现，这些程序可作为CCP 4软件套件的一部分使用。
This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes’ theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function—the only link between model parameters and observed data—is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and “true” maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programsREFMAC5,ProSMARTandLORESTR, which are available as part of theCCP4software suite.
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最小分辨率偏置电子密度图。
DOI：
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发表时间：
2008
期刊：
Acta Crystallographica Section A Foundations of Crystallography
影响因子：
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作者：
A. Altomare;C. Cuocci;C. Giacovazzo;Gihan Kamel;A. Moliterni;R. Rizzi
通讯作者：
R. Rizzi
一致。
DOI：
10.1097/iae.0000000000001602
发表时间：
2017
期刊：
Retina (Philadelphia, Pa.)
影响因子：
--
作者：
Todorich,Bozho;Thanos,Aristomenis;Yonekawa,Yoshihiro;Thomas,BenjaminJ;Faia,LisaJ;Chang,Emmanuel;Shulman,Julia;Olsen,KarlR;Blair,MichaelP;Shapiro,MichaelP;Ferrone,Philip;Vajzovic,Lejla;Toth,CynthiaA;Lee,ThomasC;Robinson,
通讯作者：
Robinson,
DOI：
10.1107/s1399004713034160
发表时间：
2014-04
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Rinaldelli M;Ravera E;Calderone V;Parigi G;Murshudov GN;Luchinat C
通讯作者：
Luchinat C
[23] 结构确定的贝叶斯统计观点：基本概念和示例。
影响因子：
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作者：
G. Bricogne
通讯作者：
G. Bricogne
DOI：
10.1038/nsb1001-899
发表时间：
2001-10-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
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作者：
Tereshko, V;Teplova, T;Egli, M
通讯作者：
Egli, M