CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures.
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures.
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CSSR：将二级结构分配到粗粒RNA三级结构。
DOI：
10.1107/s2059798322001292
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发表时间：
2022-04-01
期刊：
影响因子：
--
通讯作者：
Pyle AM
中科院分区：
文献类型：
--
作者：
Zhang C;Pyle AM
CSSR算法是一种将二级结构分配给缺失原子的RNA三维结构的算法。碱基对分配精度接近90%的三维结构，其中每个核苷酸只有一个原子可以经验识别。RNA二级结构（rSS）分配是RNA三维结构分析中最常规的形式之一。然而，传统的rSS分配程序需要单个RNA核苷酸的全原子结构。这阻碍了它们在缺少碱基原子的RNA结构建模中的应用。为了解决这一问题，开发了一种用于核碱基原子位置不完整的结构的rSS分配算法——粗粒度RNA二级结构（CSSR）。使用CSSR，即使对于每个核苷酸只有一个主链原子的RNA结构，也能实现约90%的rSS分配精度。因此，CSSR将有助于分析实验确定和计算预测的RNA 3D结构。CSSR的源代码可从https://github.com/pylelab/CSSR获得。
CSSR, an algorithm for assigning secondary structures to RNA 3D structures with missing atoms, has been developed. The base-pair assignment accuracy is close to 90% for 3D structures in which only one atom per nucleotide can be empirically identified. RNA secondary-structure (rSS) assignment is one of the most routine forms of analysis of RNA 3D structures. However, traditional rSS assignment programs require full-atomic structures of the individual RNA nucleotides. This prevents their application to the modeling of RNA structures in which base atoms are missing. To address this issue, Coarse-grained Secondary Structure of RNA (CSSR), an algorithm for the assignment of rSS for structures in which nucleobase atomic positions are incomplete, has been developed. Using CSSR, an rSS assignment accuracy of ∼90% is achieved even for RNA structures in which only one backbone atom per nucleotide is known. Thus, CSSR will be useful for the analysis of experimentally determined and computationally predicted RNA 3D structures alike. The source code of CSSR is available at https://github.com/pylelab/CSSR.
使用序列编码的裂解剂和通过离散分子动力学的细化，天然样的RNA三级结构。
影响因子：
15
作者：
Gherghe, Costin M.;Leonard, Christopher W.;Ding, Feng;Dokholyan, Nikolay V.;Weeks, Kevin M.
通讯作者：
Weeks, Kevin M.