{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T07:24:57Z","timestamp":1771053897740,"version":"3.50.1"},"reference-count":79,"publisher":"American Chemical Society (ACS)","issue":"3","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006507","name":"Funda??o Oswaldo Cruz","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006507","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005283","name":"Funda??o Cearense de Apoio ao Desenvolvimento Cient?fico e Tecnol?gico","doi-asserted-by":"publisher","award":["FIO-0167-00007.01.00\/20"],"award-info":[{"award-number":["FIO-0167-00007.01.00\/20"]}],"id":[{"id":"10.13039\/501100005283","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2026,2,9]]},"DOI":"10.1021\/acs.jcim.5c01924","type":"journal-article","created":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T20:13:41Z","timestamp":1768940021000},"page":"1895-1905","source":"Crossref","is-referenced-by-count":1,"title":["Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7717-5076","authenticated-orcid":true,"given":"Jean V.","family":"Sampaio","sequence":"first","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Instituto Oswaldo Cruz","place":["Rio de Janeiro, Brazil"]},{"name":"Fiocruz","place":["Rio de Janeiro, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-8352","authenticated-orcid":true,"given":"Andrielly H. S.","family":"Costa","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Instituto Oswaldo Cruz","place":["Rio de Janeiro, Brazil"]},{"name":"Fiocruz","place":["Rio de Janeiro, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2072-157X","authenticated-orcid":true,"given":"Aline O.","family":"Albuquerque","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5113-7595","authenticated-orcid":true,"given":"J\u00falia S.","family":"Souza","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Federal University of Cear\u00e1","place":["Fortaleza, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-5320-1596","authenticated-orcid":true,"given":"Diego S.","family":"Almeida","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Instituto Oswaldo Cruz","place":["Rio de Janeiro, Brazil"]},{"name":"Fiocruz","place":["Rio de Janeiro, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7954-5326","authenticated-orcid":true,"given":"Eduardo M.","family":"Gaieta","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Instituto Oswaldo Cruz","place":["Rio de Janeiro, Brazil"]},{"name":"Fiocruz","place":["Rio de Janeiro, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3415-2152","authenticated-orcid":true,"given":"Matheus V.","family":"Almeida","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Federal University of Cear\u00e1","place":["Fortaleza, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5613-7194","authenticated-orcid":true,"given":"Geraldo R.","family":"Sartori","sequence":"additional","affiliation":[{"name":"S\u00e3o Carlos Institute of Physics","place":["S\u00e3o Carlos, Brazil"]},{"name":"University of S\u00e3o Paulo","place":["S\u00e3o Carlos, Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1534-9857","authenticated-orcid":true,"given":"Jo\u00e3o H. M.","family":"Silva","sequence":"additional","affiliation":[{"name":"Laboratory of Structural and Functional Biology Applied to Biopharmaceuticals","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]},{"name":"Instituto Oswaldo Cruz","place":["Rio de Janeiro, Brazil"]},{"name":"Fiocruz","place":["Rio de Janeiro, Brazil"]},{"name":"Pasteur-Fiocruz Center on Immunology and Immunotherapy","place":["Eus\u00e9bio, Brazil"]},{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Fiocruz Cear\u00e1","place":["Eus\u00e9bio, Brazil"]}]}],"member":"316","published-online":{"date-parts":[[2026,1,20]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2023.2297450"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae307"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1016\/j.tips.2022.12.005"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006112"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00610-23"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.3390\/antib7030023"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abp9540"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae492"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","unstructured":"Bennett, N. R.; Watson, J. L.; Ragotte, R. J.; Borst, A. J.; See, D. L.; Weidle, C.; Biswas, R.; Shrock, E. L.; Leung, P. J. Y.; Huang, B.; Goreshnik, I.; Ault, R.; Carr, K. D.; Singer, B.; Criswell, C.; Vafeados, D.; Garcia Sanchez, M.; Kim, H. M.; V\u00e1zquez Torres, S.; Chan, S.; Baker, D.Atomically Accurate de Novo Design of\n                      Single-Domain Antibodies\n                      2024 10.1101\/2024.03.14.585103.","DOI":"10.1101\/2024.03.14.585103"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2024.2362775"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38328-5"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2025.2528902"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","unstructured":"Wohlwend, J.; Corso, G.; Passaro, S.; Getz, N.; Reveiz, M.; Leidal, K.; Swiderski, W.; Atkinson, L.; Portnoi, T.; Chinn, I.; Silterra, J.; Jaakkola, T.; Barzilay, R. Boltz-1 Democratizing Biomolecular Interaction Modeling\n                      bioRxiv\n                      2025 10.1101\/2024.11.19.624167.","DOI":"10.1101\/2024.11.19.624167"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","unstructured":"Discovery, C.; Boitreaud, J.; Dent, J.; McPartlon, M.; Meier, J.; Reis, V.; Rogozhnikov, A.; Wu, K. Chai-1: Decoding the Molecular Interactions of Life\n                      bioRxiv\n                      2024 10.1101\/2024.10.10.615955.","DOI":"10.1101\/2024.10.10.615955"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2025.2545601"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540120509"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1800708"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae618"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.839407"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.65117"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.00462"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1158\/2326-6066.CIR-14-0029"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv552"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2008.05.022"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04964-5"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.2307\/1943563"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1056"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad400"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.07.001"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/13.3.149"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.3390\/antib8040055"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.728694"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/gzq043"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1002\/prot.25964"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-04927-7"},{"key":"ref37\/cit37","unstructured":"Schr\u00f6dinger, L. L. C.\n                      The PyMOL Molecular Graphics System\n                      ; Version 2.6; PyMOL."},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01153"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20290"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab762"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00125"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2021.01.005"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2016.1190060"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1002\/pro.2874"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","unstructured":"Kelow, S.; Faezov, B.; Xu, Q.; Parker, M.; Adolf-Bryfogle, J.; Dunbrack, R. L. A Penultimate Classification of Canonical Antibody CDR Conformations\n                      bioRxiv\n                      2022 10.1101\/2022.10.12.511988.","DOI":"10.1101\/2022.10.12.511988"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2020.1840005"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.630034"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.675655"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1038\/gene.2012.28"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1111\/j.1742-4658.2006.05232.x"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh435"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty635"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00653"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","unstructured":"Dunbrack, R. L. Res ipSAE Loquunt: What\u2019s Wrong with AlphaFold\u2019s ipTM Score and How to Fix It\n                      bioRxiv\n                      2025 10.1101\/2025.02.10.637595.","DOI":"10.1101\/2025.02.10.637595"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra043186"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejca.2010.05.003"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1038\/nature01392"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1093\/gpbjnl\/qzae007"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006182"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.0c00226"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2019.10.011"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.169"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts493"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0909775106"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00167"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1002\/jmr.2158"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbt.2020.09.002"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1002\/jmr.2693"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1186\/s40364-024-00565-1"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.3816\/CBC.2008.n.002"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-021-00699-9"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","unstructured":"Chinery, L.; Hummer, A. M.; Mehta, B. B.; Akbar, R.; Rawat, P.; Slabodkin, A.; Quy, K. L.; Lund-Johansen, F.; Greiff, V.; Jeliazkov, J. R.; Deane, C. M. Baselining the Buzz Trastuzumab-HER2 Affinity, and Beyond\n                      bioRxiv\n                      2024 10.1101\/2024.03.26.586756.","DOI":"10.1101\/2024.03.26.586756"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.14348\/molcells.2016.2235"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1002\/jmr.2818"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adu9945"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.01760"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-021-03085-w"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23137314"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.884110"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01924","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01924","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T09:12:51Z","timestamp":1770628371000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c01924"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,20]]},"references-count":79,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,2,9]]}},"alternative-id":["10.1021\/acs.jcim.5c01924"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c01924","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,20]]}}}