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(A) Energy distribution of the distance between N9 of adenine and N1 of uracil. (B) Diagram of the three representative distance between N9 of adenine and N1 of uracil.

(A) Sequence, secondary structure and 3D structure of 1AFX. (B) Base-stacking energies between adjacent two nucleotides in 1AFX calculated by 3dRNAscore. '1-2' means base-stacking energy between the first and the second nucleotide, '2-3' means the second to the third ... and so on. The lower the energy, the better the base-stacking. (C) Basepairing energies between each possible base-pair in 1AFX calculated by 3dRNAscore. The lower the energy, the better the base-pairing.

References:
  1. Wang, J., et al., 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures . Nucleic Acids Res, 2015. 43(10): p. e63.