Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

Structural features captured by the KB potential. The plots (A–C) show the potentials for specific atom pairs. In each plot, the corresponding force is shown in the inset. (A) gC4-gC4 potential showing a base-stacking well ∼4.4 Å labeled (1). (B) uC4-uC4 potential showing no base-stacking well. (C) gO6-cN4 potential showing a deep base-pairing well (2a) and various structural wells (2b and 2c). (D) Distances represented in the different wells shown on the Rev binding element of HIV-1 structure (PDB id: 1duq).