We developed a novel approach for modeling antibodies in complex with their corresponding antigens, and incorporated it as an Advanced function of the ClusPro Server. The Antibody-Epitope Mapping (AbEMap) Server allows the user to predict antibody-antigen interactions with three types of inputs: (i) X-ray structures, (ii) computationally predicted structures, and (iii) simply amino acid sequences. The details of processing these three input types and differences in efficiencies are discussed in this publication in Nature Protocols.