FIGURE 2.
Energy as a function of RMSD for decoys generated by normal modes for six RNA structures (more in Supplemental Fig. 3). Scoring using our two KB potentials (all-atom on left, coarse-grained in middle) and Rosetta (right) are shown. Native scores are represented as white circles. A funnel toward low RMSD is seen in most cases. However, in several instances, some decoys score better than the native structure, a behavior that is more pronounced for the Rosetta scoring function.
