Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland.
Int J Mol Sci. 2022 Aug 25;23(17):9630. doi: 10.3390/ijms23179630.
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
RNA 是一种独特的生物分子，参与多种基本的生物学功能，所有这些功能都仅依赖于其结构和动态。由于晶体 RNA 结构的实验确定很费力，因此计算 3D 结构预测方法正在不断蓬勃发展。这些方法可以产生许多模型；因此，有必要进行比较并提取常见的结构基序，以便进一步进行医学或生物学研究。在这里，我们介绍了一个专门用于无参考的高通量 3D RNA 结构比较分析的计算管道。我们展示了它在 RNA-Puzzles 挑战赛中的应用，其中五个参赛小组试图预测 SARS-CoV-2 基因组 5'和 3'非翻译区（UTR）的三维结构。我们报告了这个难题的结果，并讨论了从分析中获得的结构基序。管道中包含的所有模拟模型和工具都可供科学和学术使用。
