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This is not a problem of algorithms but of assumptions: mimotopes recapitulate native epitope recognition through compensatory interaction networks that preserve binding energetics, without conserving sequence or surface geometry. Predictors trained on sequence similarity or static interface geometry therefore miss the residues that drive recognition. We present a physics-based workflow that refines antibody-bound mimotope conformations by microsecond-scale molecular dynamics and maps the resulting structures onto the cognate antigen using Folddisco. Across four antibody\u2013antigen systems with crystallographically defined epitopes, the workflow reaches 60 to 100% precision in epitope localization and recovers 100% of mutagenesis- or structurally validated functional hotspots, compared with at most 25% for three widely used benchmarks (EpiSearch, ClusPro, SEPPA-mAb). For the clinically relevant ChiLob 7\/4 system, it further identifies a minimal tetrapeptide (PWVP) sufficient for antibody recognition, validated by Western blot and immunoprecipitation. By grounding epitope prediction in experimentally selected binding information and energy-resolved conformational refinement, the workflow connects phage display to mechanistic structural insight.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c01562","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T22:51:20Z","timestamp":1788303080000},"page":"11259-11274","source":"Crossref","is-referenced-by-count":0,"title":["Mimotope-Guided\nMolecular Dynamics Enables Precise\nFunctional Epitope Mapping"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-6727-5400","authenticated-orcid":true,"given":"Zigan","family":"Sha","sequence":"first","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2439-6241","authenticated-orcid":true,"given":"Zheyao","family":"Hu","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjing","family":"Du","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3721-9634","authenticated-orcid":true,"given":"Jordi","family":"Marti","sequence":"additional","affiliation":[{"name":"Polytechnic University of Catalonia-Barcelona Tech , , B4\u2212B5 Northern Campus , , ,","place":["Barcelona, Catalonia, Spain, 08034"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1355-6070","authenticated-orcid":true,"given":"Gustav N.","family":"Sundell","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]},{"name":"TongRen Hospital, Shanghai Jiao Tong University School of Medicine , No. 1111 Xianxia Road , Changning District, ,","place":["Shanghai, China, 200000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu-Juan","family":"Guo","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9210-1823","authenticated-orcid":true,"given":"Sheng-Ce","family":"Tao","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , No. 800 Dongchuan Road , Minhang, ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"issue":"7491","key":"2026091409062469600_cit1","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nature12966","article-title":"Proof of principle for epitope-focused vaccine design","volume":"507","author":"Correia","year":"2014","journal-title":"Nature"},{"issue":"1","key":"2026091409062469600_cit2","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1038\/s41467-025-67361-9","article-title":"De novo\ndesign of epitope-specific antibodies via a\nstructure-driven computational workflow","volume":"17","author":"Wu","year":"2025","journal-title":"Nat.\nCommun."},{"issue":"22","key":"2026091409062469600_cit3","doi-asserted-by":"publisher","first-page":"14116","DOI":"10.1073\/pnas.202485799","article-title":"A simple physical model\nfor binding energy hot spots in protein\u2013protein\ncomplexes","volume":"99","author":"Kortemme","year":"2002","journal-title":"Proc. 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