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. Author manuscript; available in PMC: 2018 Nov 24.
Published in final edited form as: J Mol Biol. 2017 Oct 5;429(23):3587–3605. doi: 10.1016/j.jmb.2017.09.017

Figure 4. 2D and 3D tree graphs for a fragment of ribosomal RNA (PDB ID: 1DK1).

Figure 4

(a) Secondary structure. (b) Corresponding 2D tree graph topology. (c) 3D tree graph constructed from the 2D tree graph by adding extra vertices for internal loop with one nucleotide (smaller blue vertex) and helical ends (green vertices) (d) 3D tree graph corresponding to the experimentally solved tertiary structure.