RNA Structure Refinement Using the ERRASER-Phenix Pipeline
RNA Structure Refinement Using the ERRASER-Phenix Pipeline
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DOI：
10.1007/978-1-4939-2763-0_17
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发表时间：
2016-01-01
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影响因子：
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通讯作者：
Das, Rhiju
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文献类型：
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作者：
Chou, Fang-Chieh;Echols, Nathaniel;Das, Rhiju
RNA晶体学的最后一步是将坐标拟合到电子密度图中。RNA中大量的主链原子提出了一个困难而乏味的挑战，特别是在实验密度较低的情况下。ERRASER-Phenix管道可以基于原子水平RNA相互作用的物理现实模型自动改进初始RNA坐标集。该管道将基于衍射的phoenix细化与基于Rosetta的实空间细化协议ERRASER（在Rosetta下由电子密度辅助的枚举实空间细化）结合在一起。ERRASER和phoenix的结合可以提高RNA晶体学模型的几何质量，同时保持或改善与衍射数据的拟合（以R-free测量）。在这里，我们提供了一个完整的教程，通过Phenix GUI运行ERRASER-Phenix，从命令行，并通过一个应用程序在Rosetta在线服务器，包括每个人（ROSIE）。
The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by R-free). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).