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[Preprint]. 2022 Jan 4:rs.3.rs-1160075. [Version 1] doi: 10.21203/rs.3.rs-1160075/v1

Figure 2:

Figure 2:

Representative structures for the three FSE conformations. The 77-nt 3_6 pseudoknot (largest MD cluster center structure from RNAComposer) has Stems 1 and 2 coaxially stacked. The 87-nt 3_3 pseudoknot (iFoldRNA) has Stems 1 and 3 coaxially stacked. The 77-nt 3_5 junction (SimRNA) has Stems 1 and 2 coaxially stacked. The 2D structures are extracted using 3DNA-DSSR,46 and the numbers of hydrogen bonds formed in the stems (averaged over the last 500 ns of the simulations) are calculated using Gromacs.47