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The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures.
(Ge and Zhang, 2015) STAR3D: a stack-based RNA 3D structural alignment tool. Nucleic Acids Research.