New in silico approach to assessing RNA secondary structures with non-canonical base pairs.
New in silico approach to assessing RNA secondary structures with non-canonical base pairs.
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DOI：
10.1186/s12859-015-0718-6
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发表时间：
2015-09-02
影响因子：
3
通讯作者：
Szachniuk M
中科院分区：
文献类型：
--
作者：
Rybarczyk A;Szostak N;Antczak M;Zok T;Popenda M;Adamiak R;Blazewicz J;Szachniuk M
RNA的功能很大程度上取决于它的结构，因此在组织的每一个层次上正确识别这种结构是非常重要的。一个特别值得关注的是评估碱基间的相互作用，描述为二级结构，这方面的知识大大有助于解释RNA的功能，并允许在三级水平上进行结构分析。RNA二级结构可以使用通常用实验数据调整的计算机模拟方法从序列中预测，或者从3D结构原子坐标中评估。计算方法通常只考虑典型的，沃森-克里克和摆动碱基对。处理非典型的相互作用，重要的RNA结构的完整描述，仍然是非常困难的。我们介绍我们的新方法来评估一个扩展的RNA二级结构，其特点是典型和非典型的碱基对，沿着与他们的类型分类。它基于从用户提供的序列或仅描述规范碱基对的二级结构预测RNA 3D结构，然后从原子坐标导出扩展的二级结构。在我们的示例实现中，这是通过在计算管道中集成两种全自动高保真方法的功能来实现的：用于3D RNA结构预测的RNAComposer和用于碱基对注释的RNApdbee。所提出的方法将现有的RNA 3D结构预测和碱基对注释的应用联系在一起。应用RNAComposer和RNApdbee的示例性能表明，与直接预测RNA二级结构的比较方法相比，非规范碱基对评估的准确性更高。本文的在线版本（doi：10.1186/s12859-015-0718-6）包含补充材料，可供授权用户使用。
The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base-base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico methods often adjusted with experimental data, or assessed from 3D structure atom coordinates. Computational approaches typically consider only canonical, Watson-Crick and wobble base pairs. Handling of non-canonical interactions, important for a full description of RNA structure, is still very difficult. We introduce our novel approach to assessing an extended RNA secondary structure, which characterizes both canonical and non-canonical base pairs, along with their type classification. It is based on predicting the RNA 3D structure from a user-provided sequence or a secondary structure that only describes canonical base pairs, and then deriving the extended secondary structure from atom coordinates. In our example implementation, this was achieved by integrating the functionality of two fully automated, high fidelity methods in a computational pipeline: RNAComposer for the 3D RNA structure prediction and RNApdbee for base-pair annotation. The presented methodology ties together existing applications for RNA 3D structure prediction and base-pair annotation. The example performance, applying RNAComposer and RNApdbee, reveals better accuracy in non-canonical base pair assessment than the compared methods that directly predict RNA secondary structure. The online version of this article (doi:10.1186/s12859-015-0718-6) contains supplementary material, which is available to authorized users.