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. Author manuscript; available in PMC: 2020 Jun 1.
Published in final edited form as: Methods. 2019 Apr 2;162-163:60–67. doi: 10.1016/j.ymeth.2019.04.003

Figure 3.

Figure 3.

The two NMR-observed conformations for the HIV-1 stem-loop 1 [104]. The left is the major conformation and the right is the minor conformation. Interestingly, RNAstructure predicts the left structure as the lowest free energy structure and the right structure as the maximum expected accuracy (MEA) structure [56, 78, 105]. In this case, the fluctuating pairs are displaced by two nucleotides on one side (i.e. pairs from nucleotides 9 and 10 to nucleotides 25 and 26 switch to pairs to nucleotides 27 and 28).