Antigen-antibody interaction is the study of the binding interface of antigen and antibody. This knowledge facilitates antibody design and vaccine development and enhances our understanding of the molecular mechanism of pathogenicity. To predict the interacting regions between antigen and antibody, we use the RosettaDock framework within the Rosetta Suite. We also integrate sparse experimental data (i.e. hydrogen-deuterium mass spectrometry) into our docking protocol to increase the certainty of our antibody-antigen complex models. The hybrid approach enables us to achieve medium-to-high throughput structural characterization of Ab-Ag interaction. This is very useful in novel Ab discovery and vaccine design, especially in urgent public health situations.