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. 2014 Aug 1;141(5):055101. doi: 10.1063/1.4890656

FIG. 1.

FIG. 1.

The 2D (a1, a2, b1, b2) and 3D (c1, c2, d1, d2) structures of the folded (pseudoknot: a1, b1, c1, d1) and the intermediate (hairpin: a2, b2, c2, d2) states of two pseudoknot-forming RNAs: BWYV (a1, a2, c1, c2) and T2 RNA (b1, b2, d1, d2). The PDB codes of the 3D structures are 437D for the BWYV pseudoknot (c1)58 and 2TPK for the T2 pseudoknot (d1),59 respectively. (c2) and (d2) show the conformational ensembles of the intermediate states. Each conformational ensemble contains 100 conformations extracted from a MD trajectory.