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. 2018 May 25;4(5):eaar5316. doi: 10.1126/sciadv.aar5316

Fig. 2. SWM recovers noncanonical base pairs ab initio for complex RNA motifs.

Fig. 2

From left to right in each panel: 2D diagram with problem definition, 2D diagram with experimental noncanonical base pairs, experimental 3D model, SWM 3D model, and 3D overlay (experimental, marine; SWM model, salmon). (A to H) Motifs are (A) most conserved domain of human signal-recognition particle (PDB ID: 1LNT); (B) noncanonical junction from human thymidylate synthase regulatory motif, RNA-Puzzle 1 (PDB ID: 3MEI); (C) irregular J5/5a hinge from the P4-P6 domain of the Tetrahymena group I self-splicing intron (PDB ID: 2R8S); (D) P2-P3-P6 three-way A-minor junction from the Varkud satellite nucleolytic ribozyme, RNA-Puzzle 7 (PDB ID: 4R4V); (E) tertiary contact stabilizing the Schistosoma hammerhead nucleolytic ribozyme (PDB ID: 2OEU); (F) tetraloop/receptor tertiary contact from the P4-P6 domain of the Tetrahymena group I self-splicing intron (PDB ID: 2R8S); (G) T-loop/purine interaction from yeast tRNAphe involving three chemically modified nucleotides (PDB ID: 1EHZ); and (H) RNA quadruplex including an inosine tetrad (PDB ID: 2GRB). Colors indicate accurately recovered noncanonical features (pastel colors), accurately recovered extrahelical bulges (wheat with white side chains), flanking helices built de novo (violet), parts of experimental structure used for modeling but allowed to minimize (dark violet), fixed context from experimental structure (black in 2D and white in 3D), and additional helical context not included in modeling (gray in 2D and white in 3D).