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Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

机译:将基于知识的完整原子细节实例化为粗粒RNA 3D结构模型

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摘要

>Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.>Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87–3.31 Å RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 Å RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure.>Availability: Code for the C2A method, as well as the examples discussed in this article, are freely available at .>Contact:
机译:>动机:使用粗粒度方法对RNA 3D结构进行建模的方法的最新发展提出了桥接低分辨率和高分辨率建模方法的需求。尽管它们包含拓扑信息,但是粗粒模型缺少原子细节,这限制了它们在某些应用中的实用性。>结果:我们已经开发出一种将完整原子细节添加到RNA 3D结构的粗粒模型中的方法。我们的方法[粗原子(C2A)]使用在已知RNA晶体结构中观察到的几何形状。我们的方法从取自晶体结构的理想粗晶粒主链重建到完整原子晶体结构的1.87–3.31ÅRMSD之内的完整原子细节。当从建模工具NAST生成的粗粒度模型开始时,我们的方法将建立在起始结构1.00ÅRMSD范围内的完整原子结构。由此产生的完整原子结构可以用作更高分辨率建模的起点,从而将高分辨和低分辨率方法桥接到RNA 3D结构建模中。>可用性: C2A方法的代码以及本文讨论的示例可从以下网址免费获得。>联系方式:

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