Comparisons of energy versus rmsd (red) and free energy versus rmsd (green) plots for cases with disordered termini but not disordered internal loops.

<p>The points in the plots represent Rosetta generated protein structure models. In column 1 and 3, the y axis is the Rosetta all-atom energy, and in columns 2 and 4, the free energy computed using Eq. (1) with structure derived assignment of disorder/order. On the x-axis is the C<i>α</i>RMSD deviation (core RMSD) to the folded portion of native structure. Black arrows highlight regions where the free energy landscape provides improved discrimination; blue arrows, where discrimination is equivalent.