{"entity": "researcher", "timestamp": "2026-08-20T21:19:14.906Z", "family": "Ovchinnikov", "given": "Sergey", "initials": "S", "orcid": "0000-0003-2774-2744", "affiliations": ["Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA, USA. so@fas.harvard.edu."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7"}}, "publications": [{"entity": "publication", "iuid": "76136dad3c65455eb4dd2347eafd3b24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76136dad3c65455eb4dd2347eafd3b24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76136dad3c65455eb4dd2347eafd3b24"}}, "title": "A structural biology community assessment of AlphaFold2 applications.", "authors": [{"family": "Akdel", "given": "Mehmet", "initials": "M"}, {"family": "Pires", "given": "Douglas E V", "initials": "DEV"}, {"family": "Pardo", "given": "Eduard Porta", "initials": "EP"}, {"family": "J\u00e4nes", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-2540-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c4858a6ab9448695b233e09ff58698.json"}}, {"family": "Zalevsky", "given": "Arthur O", "initials": "AO", "orcid": "0000-0001-6987-8119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fdb6c4d5c9b4feb83952a3674708a12.json"}}, {"family": "M\u00e9sz\u00e1ros", "given": "B\u00e1lint", "initials": "B"}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Good", "given": "Lydia L", "initials": "LL", "orcid": "0000-0001-5308-8542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b413593ce63451b9e3a3e79cbd20a53.json"}}, {"family": "Laskowski", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-5528-0087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b0e4268b73b406d823b6b66059f2a53.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"family": "Serra", "given": "Victoria Ruiz", "initials": "VR", "orcid": "0000-0003-3991-0514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e03258443954d6d978ce8efb02a37b6.json"}}, {"family": "Rodrigues", "given": "Carlos H M", "initials": "CHM", "orcid": "0000-0002-4420-6401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642dc0c5ff09491d8e1e55449e251b80.json"}}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Borkakoti", "given": "Neera", "initials": "N"}, {"family": "Velankar", "given": "Sameer", "initials": "S", "orcid": "0000-0002-8439-5964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30f88888429c46d698e49f80e79c3083.json"}}, {"family": "Frost", "given": "Adam", "initials": "A", "orcid": "0000-0003-2231-2577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b31e4961e0c457c85f8b0729a492a57.json"}}, {"family": "Basquin", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Bateman", "given": "Alex", "initials": "A", "orcid": "0000-0002-6982-4660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e1775e560147c2b7c40e1ba7d95a4e.json"}}, {"family": "Kajava", "given": "Andrey V", "initials": "AV", "orcid": "0000-0002-2342-6886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5dfbae9ca6144d0381bf58f16029dcfe.json"}}, {"family": "Valencia", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-8937-6789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80973e7b48094490adf93726d44c49b1.json"}}, {"family": "Ovchinnikov", "given": "Sergey", "initials": "S", "orcid": "0000-0003-2774-2744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Ascher", "given": "David B", "initials": "DB", "orcid": "0000-0003-2948-2413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d141d7d1cbad4e87aef2a8878a845872.json"}}, {"family": "Thornton", "given": "Janet M", "initials": "JM", "orcid": "0000-0003-0824-4096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af0a3c9c4f12412d9709e6065c8d0813.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbb4780925604932b0853a1f8ad75145.json"}}, {"family": "Stein", "given": "Amelie", "initials": "A", "orcid": "0000-0002-5862-1681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b99e2fc33a714b929e442e312f7513f1.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Croll", "given": "Tristan I", "initials": "TI", "orcid": "0000-0002-3514-8377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c79d83429041ee8f4f47e6e4fa55f9.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "29", "issue": "11", "pages": "1056-1067", "issn-l": "1545-9985"}, "abstract": "Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.", "doi": "10.1038/s41594-022-00849-w", "pmid": "36344848", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9663297"}, {"db": "pii", "key": "10.1038/s41594-022-00849-w"}], "notes": [], "created": "2026-08-20T09:03:48.315Z", "modified": "2026-08-20T09:03:49.089Z"}, {"entity": "publication", "iuid": "ac4436481a8e4c5fa3c6f8589d010029", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4436481a8e4c5fa3c6f8589d010029.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac4436481a8e4c5fa3c6f8589d010029"}}, "title": "A structural biology community assessment of AlphaFold 2 applications", "authors": [{"family": "Akdel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-6092-3494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adcc39b269804e179cbea223cc8dc83d.json"}}, {"family": "Pires", "given": "Douglas E V", "initials": "DEV", "orcid": "0000-0002-3004-2119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/536bf1b7030d40a49643ccaa4e6a6c8e.json"}}, {"family": "Porta Pardo", "given": "Eduard", "initials": "E", "orcid": "0000-0001-7900-4239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3705290c0dc44526afe59c6837df09c2.json"}}, {"family": "J\u00e4nes", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0002-2540-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c4858a6ab9448695b233e09ff58698.json"}}, {"family": "Zalevsky", "given": "Arthur O", "initials": "AO", "orcid": "0000-0001-6987-8119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fdb6c4d5c9b4feb83952a3674708a12.json"}}, {"family": "M\u00e9sz\u00e1ros", "given": "B\u00e1lint", "initials": "B", "orcid": "0000-0003-0919-4449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5847cba0f8f43e6b6827a40ddf47f2c.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Good", "given": "Lydia L", "initials": "LL", "orcid": "0000-0001-5308-8542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b413593ce63451b9e3a3e79cbd20a53.json"}}, {"family": "Laskowski", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-5528-0087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b0e4268b73b406d823b6b66059f2a53.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Ruiz Serra", "given": "Victoria", "initials": "V", "orcid": "0000-0003-3991-0514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e03258443954d6d978ce8efb02a37b6.json"}}, {"family": "Rodrigues", "given": "Carlos H M", "initials": "CHM"}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Borkakoti", "given": "Neera", "initials": "N", "orcid": "0000-0002-5878-1490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13aef1cd03bd4ed0803d58e78851fad4.json"}}, {"family": "Velankar", "given": "Sameer", "initials": "S"}, {"family": "Frost", "given": "Adam", "initials": "A", "orcid": "0000-0003-2231-2577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b31e4961e0c457c85f8b0729a492a57.json"}}, {"family": "Lindorff-Larsen", "given": "Kresten", "initials": "K", "orcid": "0000-0002-4750-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd1f0559c6d4d58a1459dd38f851c93.json"}}, {"family": "Valencia", "given": "Alfonso", "initials": "A"}, {"family": "Ovchinnikov", "given": "Sergey", "initials": "S", "orcid": "0000-0003-2774-2744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c1c152b72314d178a2f01630d3ebbb7.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Ascher", "given": "David B", "initials": "DB", "orcid": "0000-0003-2948-2413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d141d7d1cbad4e87aef2a8878a845872.json"}}, {"family": "Thornton", "given": "Janet M", "initials": "JM", "orcid": "0000-0003-0824-4096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af0a3c9c4f12412d9709e6065c8d0813.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbb4780925604932b0853a1f8ad75145.json"}}, {"family": "Stein", "given": "Amelie", "initials": "A", "orcid": "0000-0002-5862-1681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b99e2fc33a714b929e442e312f7513f1.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Croll", "given": "Tristan I", "initials": "TI", "orcid": "0000-0002-3514-8377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71c79d83429041ee8f4f47e6e4fa55f9.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2021-09-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.09.26.461876", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:06:50.640Z", "modified": "2026-08-20T10:06:50.965Z"}]}