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Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computational protocol that uses template\u2010based modeling and docking to predict epitope residues. This protocol is implemented in three major steps. First, a template\u2010based modeling approach is used to build the antibody structures. We tested several options, including generation of models using AlphaFold2. Second, each antibody model is docked to the antigen using the fast Fourier transform (FFT) based docking program PIPER. Attention is given to optimally selecting the docking energy parameters depending on the input data. In particular, the van der Waals energy terms are reduced for modeled antibodies relative to x\u2010ray structures. Finally, ranking of antigen surface residues is produced. The ranking relies on the docking results, that is, how often the residue appears in the docking poses' interface, and also on the energy favorability of the docking pose in question. The method, called PIPER\u2010Map, has been tested on a widely used antibody\u2013antigen docking benchmark. The results show that PIPER\u2010Map improves upon the existing epitope prediction methods. An interesting observation is that epitope prediction accuracy starting from antibody sequence alone does not significantly differ from that of starting from unbound (i.e., separately crystallized) antibody structure.<\/jats:p>","DOI":"10.1002\/prot.26420","type":"journal-article","created":{"date-parts":[[2022,9,11]],"date-time":"2022-09-11T11:58:07Z","timestamp":1662897487000},"page":"171-182","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Mapping of antibody epitopes based on docking and homology modeling"],"prefix":"10.1002","volume":"91","author":[{"given":"Israel T.","family":"Desta","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering Boston University  Boston Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei","family":"Kotelnikov","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics and Statistics Stony Brook 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