RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data

[Display omitted] •A Rosetta method incorporating HDX-MS data to model Ab-Ag complexes is introduced.•HDX-MS-guided sampling generated more near-native models for all benchmark complexes.•Docking performance is improved with as little as one HDX interacting peptide.•Results from docking with HDX can uncover allosteric peptides. High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function and enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually. By incorporating HDX data as both distance restraints and a scoring term in the RosettaDock algorithm, RosettaHDX successfully generated near-native models (interface root-mean square deviation ≤ 4 Å) for all 9 benchmark complexes examined, averaging 3.6 times more near-native models than Rosetta alone. Near-native models among the top 10 scoring were identified in 3/9 cases, compared to 1/9 with Rosetta alone. Additionally, we developed a predictive metric based on docking results with HDX restraints to identify allosteric peptides in HDX datasets.