{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T16:55:15Z","timestamp":1791478515088,"version":"4.3.4"},"reference-count":20,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100010190","name":"Grand \u00c9quipement National De Calcul Intensif","doi-asserted-by":"publisher","award":["2023\u2010AD010713847R1"],"award-info":[{"award-number":["2023\u2010AD010713847R1"]}],"id":[{"id":"10.13039\/501100010190","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR\u201011\u2010INBS\u20100013"],"award-info":[{"award-number":["ANR\u201011\u2010INBS\u20100013"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["21\u2010ESRE\u20100048"],"award-info":[{"award-number":["21\u2010ESRE\u20100048"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Massive sampling with AlphaFold2 improves protein\u2013protein complex predictions. This has been shown during the last CASP15\u2010CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antibody\u2013antigen binding remain challenging. CAPRI Round 55 consisted of three antibody\u2013antigen targets and one heterotrimer. We used our AlphaFold2\u2010based MassiveFold, running 6 prediction pools, each with their own set of parameters, to produce in total more than 6000 predictions per target. We show here that massive sampling categorically produces acceptable to high quality predictions, however it is clear that the AlphaFold2 confidence score cannot be used to identify the best models in the set. We also show that, contrary to what was done before for CASP15\u2010CAPRI with AFsample, increasing the sampling without activating the dropout provides the best models for most of the targets of Round 55.<\/jats:p>","DOI":"10.1002\/prot.26802","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T08:57:06Z","timestamp":1737968226000},"page":"1768-1776","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Massive Sampling Strategy for Antibody\u2013Antigen Targets in\n                    <scp>CAPRI<\/scp>\n                    Round 55 With\n                    <scp>MassiveFold<\/scp>"],"prefix":"10.1002","volume":"94","author":[{"given":"Nessim","family":"Raouraoua","sequence":"first","affiliation":[{"name":"Univ. Lille, UMR 8576 \u2010 UGSF \u2010 Unite\u0301 de Glycobiologie Structurale et Fonctionnelle  Lille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3957-9470","authenticated-orcid":false,"given":"Marc F.","family":"Lensink","sequence":"additional","affiliation":[{"name":"Univ. Lille, UMR 8576 \u2010 UGSF \u2010 Unite\u0301 de Glycobiologie Structurale et Fonctionnelle  Lille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6807-6621","authenticated-orcid":false,"given":"Guillaume","family":"Brysbaert","sequence":"additional","affiliation":[{"name":"Univ. Lille, UMR 8576 \u2010 UGSF \u2010 Unite\u0301 de Glycobiologie Structurale et Fonctionnelle  Lille France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,1,27]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26222"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26237"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.04.463034v1"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26617"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26609"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26551"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-02130-4"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26562"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad573"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43588-024-00714-4"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01488-1"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2024.168540"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0161879"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20264"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.03021"},{"key":"e_1_2_9_19_1","first-page":"8","article-title":"The PyMOL Molecular Graphics System","volume":"1","author":"Schr\u00f6dinger L. L. C.","year":"2015","journal-title":"Version"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21123"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4865"}],"container-title":["Proteins: Structure, Function, and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.26802","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/prot.26802","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.26802","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T16:21:00Z","timestamp":1791476460000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.26802"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,27]]},"references-count":20,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["10.1002\/prot.26802"],"URL":"https:\/\/doi.org\/10.1002\/prot.26802","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.22541\/au.172592104.47153431\/v2","asserted-by":"object"},{"id-type":"doi","id":"10.22541\/au.172592104.47153431\/v1","asserted-by":"object"}]},"ISSN":["0887-3585","1097-0134"],"issn-type":[{"value":"0887-3585","type":"print"},{"value":"1097-0134","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,27]]},"assertion":[{"value":"2024-09-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-12","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-27","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}