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Coarse-grained representation of RNA. (A) Coarse-grained representation of a nucleotide by using three sites; namely, phosphate (P), sugar (S), and base (B) are given. (B) The secondary structure of the 22-nt P5GA hairpin in which the bonds formed between base pairs are labeled 1–9. The PDB structure (13) and the corresponding structure using the coarse grained model are shown on the right.
