All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

Figure 3

Sampling of calculated energy versus rmsd plots for four decoy sets. A different atomic four-body statistical potential energy function (i.e., distinct pairs of atomic alphabet size and tessellation edge-length cutoff parameters) was selected to compute the energy values for each plot. The plots reveal wide variability in the number of alternative conformations for a given native structure based on decoy category, and they highlight the relative strengths and weaknesses of native rank, correlation coefficient , -score, and fractional enrichment (FE) as performance measures under a range of conditions, hence reinforcing their collective importance for evaluating energy functions.