FIGURE 7.

Examples of antibody–antigen complex structure predictions by AlphaFold. (a) Native and top‐ranked AlphaFold model (pTM = 0.78) for PDB 4NIK (F5 antibody/human gankyrin complex). This model is of medium accuracy by CAPRI criteria (I‐RMSD = 1.52 Å). Modeled and X‐ray complex structures are colored as indicated and shown superposed by gankryin. Unresolved regions modeled by AlphaFold are not shown. (b) Native and top‐ranked AlphaFold model (pTM = 0.61) for PDB 6OAN (053054 antibody/P vivax DBP complex). This model is of medium accuracy by CAPRI criteria (I‐RMSD = 2.12 Å). Modeled and X‐ray structures are colored as indicated, shown superposed by DBP, and unresolved regions modeled by AlphaFold are not shown. (c) Native and top‐ranked AlphaFold model (pTM = 0.66) for PDB 3RJQ (A12 nanobody/HIV C186 gp120 complex), superposed by C186 gp120. This AlphaFold model does not have contacting residues between the proteins within a 5 Å distance cutoff. Structures are colored as indicated in the figure, and unresolved regions modeled by AlphaFold on C186 gp120 are shown in light green