FIGURE 1.

Antibody–antigen modeling accuracy of AlphaFold. (a) Benchmarking of AlphaFold (v.2.2, multimer model) was performed on 427 antibody–antigen complexes. For each complex, 25 predictions were generated and ranked by AlphaFold model confidence score. Antibody–antigen predictions were evaluated for complex modeling accuracy using CAPRI criteria for high, medium, and acceptable accuracy. The success rate was calculated based on the percentage of cases that had at least one model among their top N ranked predictions that met a specified level of CAPRI accuracy. Bars are colored by CAPRI accuracy level. (b) Example of a near‐native prediction by AlphaFold, in comparison with the experimentally determined structure (PDB: 6nmv; antibody/SIRP‐alpha complex). This model has high CAPRI accuracy (I‐RMSD = 0.68 Å) and has the highest model confidence of all 25 predictions of this complex (model confidence = 0.88). (c) An example of an acceptable accuracy complex model from AlphaFold, in comparison with the experimentally determined structure (PDB: 6j15; antibody/PD‐1 complex). This model has acceptable CAPRI accuracy (I‐RMSD = 3.35 Å), and has the highest model confidence of all 25 predictions of this complex (model confidence = 0.75). Complex structures in (b,c) are superposed by antigen with the model and the x‐ray structure components colored separately as indicated on right.