Fig. 5: Case studies of the predictions of NuFold. | Nature Communications

Fig. 5: Case studies of the predictions of NuFold.

From: NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation

Fig. 5

The native structures and predicted structures are superimposed and shown in grey and rainbow, respectively. The 5’-terminal and 3’-terminal are shown in blue and red, respectively. a tRNA-Glu of Escherichia coli (PDB: 2DER chain C). 76 nt, RMSD: 2.88 Å. b PPRP riboswitch. (PDB: 6CK4 chain A). 117 nt, RMSD: 2.64 Å. c RNA-puzzle target, rp12. ydaO riboswitch. 125 nt, RMSD: 3.55 Å. d RNA-puzzle rp06. Adenosylcobalamin riboswitch. 168 nt, RMSD: 3.10 Å. e partial structure of the 23S rRNA. (PDB: 5ML7 chain A) 96 nt. An example that improved by increasing the number of recycles. The prediction of baseline is shown on the left (RMSD: 8.70 Å) and the prediction with more recycles is on the right (RMSD 3.39 Å). f twister ribozyme. (PDB: 4OJI chain A) 54 nt. An example that improved by using a metagenome MSA and recycles. Left, the baseline model (RMSD: 4.14 Å); right, the improved model (RMSD 2.23 Å). g RNA-puzzle rp05. lariat capping ribozyme. 188 nt. Left, the native structure; center, the baseline model (RMSD: 22.2 Å); right, model using metagenome MSA with more recycles (RMSD: 11.7 Å). h CRISPR RNA. (PDB: 4U7U chain L). 61 nt, RMSD: 33.0 Å.

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