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. Author manuscript; available in PMC: 2017 Feb 27.
Published in final edited form as: J Mol Biol. 2016 Feb 17;428(5 Pt A):748–757. doi: 10.1016/j.jmb.2015.11.013

Figure 2. RNA design puzzles from Eterna demonstrate features that make design difficult.

Figure 2

Open or filled squares indicate failure or successful solutions, respectively, by existing RNA design algorithms – RNAinverse (red), INFO-RNA (yellow), RNA-SSD (green), NUPACK (cyan), DSS-Opt (blue), and MODENA (purple). [A] Stem length: Shortie 4, Shortie 6; [B] Adjacent Multiloops: Kyurem 5, Kyurem 7; [C] Loop next to a Multiloop; [D] Bulges: Just down to 1 bulge, 1,2,3 and 4 bulges; [E] Internal Loops: Mat – Lot 2-2 B, Crop Circle 2; [F] Zigzags: Hard Y; [G] Simple puzzles: This is ACTUALLY Small and Easy 6; [H] Quasispecies 2-2 Loop Challenge, Water Strider, The Fractal, Mutated Chicken Feet