Fig. 5: EModelX(+AF) demonstrated abilities to rectify the misfolded AlphaFold structures.
a The boxplot of TM-score in different resolution ranges (12, 14, 35, and 38 maps for 2–2.5, 2.5–3, 3–3.5, 3.5–4 Å, respectively). The box extends from the first quartile (Q1) to the third quartile (Q3), with a line at the median. The whiskers extend from the box to the farthest data point lying within 1.5x (Q3-Q1) from the box. Flier points are those past the end of the whiskers. b Comparison of RMSD achieved by EModelX(+AF) and AlphaFold on 660 single chains split from 99 complex structures in our test set. c Comparison of TM-score achieved by EModelX(+AF) and AlphaFold on the 82 hard targets (AlphaFold TM-score < 0.7). Blue lines represent linear function y=x. d–f: Test case EMD-23970 at 3.8 Å resolution (PDB ID: 7msw). d superimposing PDB structure (blue) with models built by EModelX(+AF), EModelX, and AlphaFold. The models are rendered by Cα distance to the PDB structure. e The Cα distance and B-factor for each residue. Each data point represents an average value of nearby five residues. f CC_mask and B-factor for each residue. g Test case EMD-30612 at 3.7 Å resolution (PDB ID: 7d84). Zooming into chain e, the PDB structure is represented as tan ribbons, the model built by EModelX(+AF) is colored red, and the superimposed AlphaFold structure is sky-blue.
