{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T04:10:04Z","timestamp":1769832604524,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T00:00:00Z","timestamp":1720569600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["802554"],"award-info":[{"award-number":["802554"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004271","name":"Sapienza University of Rome","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004271","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Identifying the binding sites of antibodies is essential for developing vaccines and synthetic antibodies. In this article, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the importance of geometric information.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Specifically, we compare different geometric deep learning methods applied to proteins\u2019 inner (I-GEP) and outer (O-GEP) structures. We incorporate 3D coordinates and spectral geometric descriptors as input features to fully leverage the geometric information. Our research suggests that different geometrical representation information is useful for different tasks. Surface-based models are more efficient in predicting the binding of the epitope, while graph models are better in paratope prediction, both achieving significant performance improvements. Moreover, we analyze the impact of structural changes in antibodies and antigens resulting from conformational rearrangements or reconstruction errors. Through this investigation, we showcase the robustness of geometric deep learning methods and spectral geometric descriptors to such perturbations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The python code for the models, together with the data and the processing pipeline, is open-source and available at https:\/\/github.com\/Marco-Peg\/GEP.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae405","type":"journal-article","created":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T12:01:23Z","timestamp":1720612883000},"source":"Crossref","is-referenced-by-count":2,"title":["Geometric epitope and paratope prediction"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-8403","authenticated-orcid":false,"given":"Marco","family":"Pegoraro","sequence":"first","affiliation":[{"name":"Department of Computer Science, Sapienza University of Rome , 00185, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7420-1294","authenticated-orcid":false,"given":"Cl\u00e9mentine","family":"Domin\u00e9","sequence":"additional","affiliation":[{"name":"Gatsby Computational Neuroscience Unit, University College London , W1T 4JG, United-Kingdom"}]},{"given":"Emanuele","family":"Rodol\u00e0","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Sapienza University of Rome , 00185, Italy"}]},{"given":"Petar","family":"Veli\u010dkovi\u0107","sequence":"additional","affiliation":[{"name":"Google-DeepMind , 6-8 Handyside Street , London N1C 4UZ, UK"}]},{"given":"Andreea","family":"Deac","sequence":"additional","affiliation":[{"name":"D\u00e9partement d\u2019informatique et de recherche op\u00e9rationelle, Universit\u00e9 de Montr\u00e9al , QC H2S 3H1, 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