{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T16:26:28Z","timestamp":1792772788563,"version":"4.5.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006507","name":"Funda\u00e7\u00e3o Oswaldo Cruz","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006507","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["405134\/2023\u20131"],"award-info":[{"award-number":["405134\/2023\u20131"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Antibody\u2013antigen (Ab\u2013Ag) interactions are central to immune recognition and widely exploited in therapeutic design, making accurate structural characterization of these complexes a central challenge in the field. While docking and artificial intelligence\u2013based approaches can generate multiple candidate binding modes, reliably identifying near\u2013native conformations represent a key bottleneck. Existing methods depend largely on static scoring functions, which fail to capture the dynamic nature of Ab\u2013Ag interfaces and, as a result, offer limited power to discriminate between competing poses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we evaluate heated molecular dynamics (HMD) as a strategy to discriminate binding pose quality based on structural stability under thermal perturbation, implemented through the automated workflow AutoHMD. Across a diverse set of Ab\u2013Ag complexes, HMD enabled clear separation between high\u2013quality and incorrect poses. During simulations, near\u2013native complexes maintained a stable interface, whereas incorrect ones showed progressive divergence, particularly at elevated temperatures. Interaction analysis revealed that high-quality poses maintain more stable and persistent interfacial contacts throughout the simulations. In contrast, incorrect poses display an unstable interaction network. Additional simulation replicates increased classification consistency, while a mean iRMSD cutoff of approximately 2.5\u2009\u00c5 achieved 90% accuracy in cross-validation and retained robust performance on an independent external set. Its transfer to Boltz-2-generated complexes further supported the broader applicability of HMD to AI-predicted binding poses. Overall, AutoHMD provides a reproducible, scalable, and high\u2013throughput framework for validation of predicted antibody\u2013antigen complexes, with potential applications in structural bioinformatics and biopharmaceutical design.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag757","type":"journal-article","created":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T11:46:39Z","timestamp":1791459999000},"source":"Crossref","is-referenced-by-count":0,"title":["AutoHMD: scalable and accurate validation of antibody\u2013antigen complexes by heated molecular dynamics"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-5113-7595","authenticated-orcid":false,"given":"Julia S","family":"Souza","sequence":"first","affiliation":[{"name":"Universidade Federal do Cear\u00e1 Departamento de Bioqu\u00edmica e Biologia Molecular, , Av. Humberto Monte s\/n , Fortaleza, Cear\u00e1, 60020-181,","place":["Brazil"]},{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2072-157X","authenticated-orcid":false,"given":"Aline O","family":"Albuquerque","sequence":"additional","affiliation":[{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-5320-1596","authenticated-orcid":false,"given":"Diego S","family":"Almeida","sequence":"additional","affiliation":[{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]},{"name":"Oswaldo Cruz Foundation (Fiocruz) Postgraduate Program in Computational and Systems Biology, , Av. Brasil, 4365 , Rio de Janeiro, Rio de Janeiro, 21040-900,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-8352","authenticated-orcid":false,"given":"Andrielly H S","family":"Costa","sequence":"additional","affiliation":[{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7717-5076","authenticated-orcid":false,"given":"Jean V","family":"Sampaio","sequence":"additional","affiliation":[{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]},{"name":"Oswaldo Cruz Foundation (Fiocruz) Postgraduate Program in Computational and Systems Biology, , Av. Brasil, 4365 , Rio de Janeiro, Rio de Janeiro, 21040-900,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1534-9857","authenticated-orcid":false,"given":"Jo\u00e3o H M","family":"Silva","sequence":"additional","affiliation":[{"name":"Fiocruz Cear\u00e1 Structural and Functional Biology in Biopharmaceuticals Group, , R. S\u00e3o Jos\u00e9, s\/n , Eus\u00e9bio, Cear\u00e1, 61773-270,","place":["Brazil"]},{"name":"Oswaldo Cruz Foundation (Fiocruz) Pasteur\u2013Fiocruz Center on Immunology and Immunotherapy, , R. 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