Fig. 5: Using AF2 to predict homo-oligomeric assemblies and their oligomeric state.

a, AF2 prediction for each oligomeric state (1–4 for monomers and dimers, and 1–5 for trimers and tetramers). Only proteins for which the monomer had pLDDT > 90 are shown. For visualization, the predicted successes (top) and failures (bottom) were separated into two plots. Success is defined when the peak of the homo-oligomeric state scan matches the annotation, or the pTMscore of the next oligomer state is substantially lower (−0.1). b, For each of the annotated assemblies, the pTMscore of monomeric prediction is compared with the max pTMscore of non-monomeric prediction. c, Monomer prediction failure. Two monomers were predicted to be homo-dimers. For the first case (PDB: 1BKZ), the prediction matched the asymmetric unit (shown as blue/green and prediction in white). For the second case (PDB: 1BWZ), the prediction matched one of the crystallographic interfaces. d, 3TDT trimer was predicted to be a tetramer. Although the interface is technically correct, for this c-symmetric protein, the pTMscore was not able to discriminate between 3 and 4 copies. e, Comparison of docking quality between AF2 (x axis) and a standard docking tool GRAMM (y axis). Comparisons were made using the DockQ score. Models with a DockQ score that was higher than 0.23 are assumed to be acceptable according to the Critical Assessment for Predicted Interactions (CAPRI) criteria (marked outside the shaded area). Black circles indicate the complex was well modeled by both methods. The average DockQ score and the number of acceptable or better models are shown in the axis labels. It should be noted here that AF2 both folds and docks the proteins, whereas GRAMM only docks them. f, Examples of AF2-predicted interactions mediated by regions of intrinsic disorder.