Assignment of beads on the four standard nucleotides and strength of base-base interactions in the different models.

A-B) Phosphate atoms are in gold, C1’ carbons from the sugar group in light green and C2 carbons from the nucleobase in dark green. A GC pair is shown in A) and an AU pair in B). The atom names are shown over white structures to enhance legibility. The assignation of the ENCoM atom types to each atom name is given in Table H in S1 Text. All three beads are included in the ENMs tested for the present work. The base pairs shown were extracted from an A-form RNA helix generated using the MC-Fold and MC-Sym pipeline [36]. C) A stack of canonical base pairs, AU over GC, extracted from PDB code 2V6W. ENCoM’s β_ij term, Cut-ANM’s binary interaction and PD-ANM’s distance dependent interaction are shown in panel D) between all pairs of nucleobase beads, from the exact structure shown in C). The parameters used are 10 Å cutoff for Cut-ANM and a power dependency of 7 for PD-ANM, the optimal values found in the present study for the B-factors benchmark. The values are rescaled to a maximum of 100 to allow better comparison of the three potentials. The cytosine is in close proximity to the diagonal adenosine, hence the high interaction value assigned by PD-ANM, proportional to the inverse of the distance to the 7^th power.