Fig. 5
From: RNA 3D structure prediction guided by independent folding of homologous sequences
Core RMSD [Å] for the best 100 models for sequences of homologs with SimRNA and Rosetta. Tar stands for “Target” sequence. Adenine riboswitch: a04 (Clostridioides difficile, AAML04000013.1), a99 (Streptococcus pyogenes, AAFV01000199.1), b28 (Oceanobacillus iheyensis, BA000028.3), u51 (Bacillus subtilis, U51115.1); c-di-GMP riboswitch: gap (Clostridium tetani, AE015927.1), gba (Bacillus halodurans, BA000004.3), gbx (Peptoclostridium difficile, ABFD02000011.1), gxx (Deinococcus radiodurans, AE000513.1); TPP riboswitch: tc5 (Xanthomonas campestris, CP000050.1), tae (Geobacter sulfurreducens, AE017180.1), tb2 (Corynebacterium diphtheriae, BX248356.1), tal (Streptococcus agalactiae, AL766847.1); THF riboswitch: tha (Marvinbryantia formatexigens, ACCL02000010.1), hak (Oribacterium sinus, ACKX01000080.1), haq (metagenome sequence, AAQK01002704.1), hcp (Natranaerobius thermophilus, CP001034.1); tRNA: taf (Tetrahymena thermophila, AF396436.1), tm5 (Rana catesbeiana, M57527.1), tab (Drosophila melanogaster, AB009835.1), tm2 (Methanothermus fervidus, M26977.1); RNA-Puzzle 13: zcp (Ralstonia pickettii, CP001644.1), znc (Bradyrhizobium sp. ORS 278, CU234118.1), zc3 (Ralstonia solanacearum, CP025741.1), zza (Caulobacter sp. K31, CP000927.1); RNA-Puzzle 14: a22 (marine metagenome, AACY022736085.1), aa2 (Synechococcus sp. JA-2-3B’a(2–13), AACY020096225.1), aj6 (Cyanophage phage, AJ630128.1), cy2 (marine metagenome, AACY023015051.1) RNA-Puzzle 17: sequences were obtained from the alignment provided by [30]: s21 (2236876011_199011), hcf (HCF12C_58327), s23 (2210131864), pis (sequence experimentally investigated in [30])