Fig. 3: Results of antibody-antigen complex structure prediction (n = 89 protein targets).
From: High-accuracy protein complex structure modeling based on sequence-derived structure complementarity
a Average TM-scores of complex structures and DockQ scores of antibody-antigen interface for the predicted models by DeepSCFold, AlphaFold-Multimer and AlphaFold3. The data are presented as the mean ± 95% CI, with n = 89 proteins from the benchmark set. b Head-to-head comparison of the TM-scores and DockQ scores on each test case between DeepSCFold, AlphaFold-Multimer and AlphaFold3, with n = 89 proteins from the benchmark set. c Example of an antibody-antigen complex (PDB ID: 8SIT) predicted by DeepSCFold and AlphaFold-Multimer, where experimental structures are colored in red and monomers of the predicted models are colored differently. d, e Predicted aligned error (PAE) plots for the antibody heavy and light chains modeled by AlphaFold-Multimer (d) and DeepSCFold (e). Source data are provided as a Source Data file.
