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. 2022 Oct 12;13:6028. doi: 10.1038/s41467-022-33729-4

Fig. 3. Analysis of assembly success using different methods.

Fig. 3

a TM-scores for the complexes that could be assembled to completion using FoldDock (FD) or AFM and predicted native dimeric, native trimeric and all trimeric subcomponents, respectively. The complete set of complexes from the three approaches (n = 108) is shown, with scores of zero representing missing complexes for each approach. The points display the TM-score of the individual complexes and the black “x” marks the average scores. The average TM-scores is 0.09 vs 0.10, 0.36 vs 0.33 and 0.47 vs 0.41 using native dimers, trimers and all trimers for FoldDock vs AFM, respectively. FoldDock thereby outperforms AFM overall. The median scores are low due to the missing complexes between the approaches. Considering only the successful assemblies using native dimers, trimers and all trimers, the median scores are 0.77, 0.80 and 0.51, respectively. b Complex scoring using all trimers as subcomponents. ROC curve, where positives (n = 30) are complete assemblies of TM-score ≥0.8, as a function of the average interface plDDT, the number of interface residues and contacts normalised with the number of chains in each complex, the average interface plDDT times the logarithm of the number of interface contacts and mpDockQ (see c). The best separators are plDDT⋅log(contacts) and mpDockQ, both with AUC 0.83. c TM-score vs the best separator in b), plDDT⋅log(contacts), coloured by the fraction of completion for the assemblies (n = 175). The solid grey line represents a sigmoidal fit creating the mpDockQ score (see Methods section). When the mpDockQ tends to be high, so does the TM-score and % completion of the complex. This suggests that mpDockQ can be used to select when a complex is complete and how accurate it is. d TM-score distribution of the complete complexes (n = 91) assembled using all FoldDock trimers and examples at different thresholds. The assembled complexes (coloured by chain) are in structural superposition with the native ones (grey). The PDB IDs for the complexes shown and their corresponding symmetries and TM-scores are 5TRM (Octahedral, 0.22), 2V5H (Dihedral, 0.45), 7JQZ (Dihedral, 0.51), 5XPB (Helical, 0.82), 2GRE (Tetrahedral, 0.97) and 5T11 (Cyclic, 0.98). At TM-score 0.8, the assembled complex is similar to the native one.