biostudies-literatureUnknownSun CPredicting Antibody-Antigen (Ab-Ag) docking and structure-based design represent significant long-term and therapeutically important challenges in computational biology. We present SAGERank, a general, configurable deep learning framework for antibody design using Graph Sample and Aggregate Networks. SAGERank successfully predicted the majority of epitopes in a cancer target dataset. In nanobody-antigen structure prediction, SAGERank, coupled with a protein dynamics structure prediction algorithm, slightly outperforms Alphafold3. Most importantly, our study demonstrates the real potential of inductive deep learning to overcome the small dataset problem in molecular science. The SAGERank models trained for antibody-antigen docking can be used to examine general protein-protein interaction tChemical sciencehttps://www.ebi.ac.uk/biostudies/studies/S-EPMC12415532biostudies-literatureSAGERank: inductive learning of protein-protein interaction from antibody-antigen recognition.PMC12415532Li XMa BSun CXu HWang YTang YBai GfalseSAGERank: inductive learning of protein-protein interaction from antibody-antigen recognition.Predicting Antibody-Antigen (Ab-Ag) docking and structure-based design represent significant long-term and therapeutically important challenges in computational biology. We present SAGERank, a general, configurable deep learning framework for antibody design using Graph Sample and Aggregate Networks. SAGERank successfully predicted the majority of epitopes in a cancer target dataset. In nanobody-antigen structure prediction, SAGERank, coupled with a protein dynamics structure prediction algorithm, slightly outperforms Alphafold3. Most importantly, our study demonstrates the real potential of inductive deep learning to overcome the small dataset problem in molecular science. The SAGERank models trained for antibody-antigen docking can be used to examine general protein-protein interaction t2025-01-01T00:00:00Z2025 Aug2026-06-02T02:28:00.316Z2026-04-13T03:12:12.126ZS-EPMC124155324092701210.1039/d5sc03707g