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Graph theoretical models of an RNA 2D structure for a three-way junction (a) by Waterman, Nussinov, Shapiro, and Schlick. (b) Waterman (1978): graphs at base-pair level; (c) Nussinov (1989): ordered labeled tree graphs B, I, H, M, and S represent bulge, internal loop, bifurcation loop, and single-stranded region, respectively; (d) Shapiro (1990): simplified tree graphs where R represent a paired region; (e) Schlick (2003): RAG tree and dual graphs.
