Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models |
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| Authors: | Julita Gumna Maciej Antczak Ryszard W. Adamiak Janusz M. Bujnicki Shi-Jie Chen Feng Ding Pritha Ghosh Jun Li Sunandan Mukherjee Chandran Nithin Katarzyna Pachulska-Wieczorek Almudena Ponce-Salvatierra Mariusz Popenda Joanna Sarzynska Tomasz Wirecki Dong Zhang Sicheng Zhang Tomasz Zok Eric Westhof Zhichao Miao Marta Szachniuk Agnieszka Rybarczyk |
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| Abstract: | 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. |
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| Keywords: | multi-model evaluation, RNA 3D structures, 3D structure prediction, reference-free analysis, SARS-CoV-2 genome, 5′ -UTR, 3′ -UTR |
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