{"entity": "researcher", "timestamp": "2026-08-20T21:05:28.984Z", "family": "Valencia", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-8937-6789", "affiliations": ["Barcelona Supercomputing Center (BSC), Barcelona, Spain. alfonso.valencia@bsc.es."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/80973e7b48094490adf93726d44c49b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/80973e7b48094490adf93726d44c49b1"}}, "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": "3b6addb33bea4a8d87ddab683fecf5dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3b6addb33bea4a8d87ddab683fecf5dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3b6addb33bea4a8d87ddab683fecf5dd"}}, "title": "COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity\u2019s fight", "authors": [{"family": "Auffray", "given": "Charles", "initials": "C", "orcid": "0000-0003-2226-7411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df19e68ad01d42d7bc2684107008b516.json"}}, {"family": "Balling", "given": "Rudi", "initials": "R"}, {"family": "Blomberg", "given": "Niklas", "initials": "N"}, {"family": "Bonaldo", "given": "Myrna C", "initials": "MC"}, {"family": "Boutron", "given": "Bertrand", "initials": "B", "orcid": "0000-0001-5241-3462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5537adf5e6148bbbe41e598e16696c2.json"}}, {"family": "Brahmachari", "given": "Samir", "initials": "S"}, {"family": "Br\u00e9chot", "given": "Christian", "initials": "C"}, {"family": "Cesario", "given": "Alfredo", "initials": "A"}, {"family": "Chen", "given": "Sai Juan", "initials": "SJ"}, {"family": "Cl\u00e9ment", "given": "Karine", "initials": "K"}, {"family": "Danilenko", "given": "Daria", "initials": "D"}, {"family": "Di Meglio", "given": "Alberto", "initials": "A"}, {"family": "Gelemanovi\u0107", "given": "Andrea", "initials": "A"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Gojobori", "given": "Takashi", "initials": "T"}, {"family": "Goldman", "given": "Jason D", "initials": "JD"}, {"family": "Goldman", "given": "Michel", "initials": "M", "orcid": "0000-0003-0222-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/063c9be1941c49a9ba4ba4840a12f0a4.json"}}, {"family": "Guo", "given": "Yi Ke", "initials": "YK"}, {"family": "Heath", "given": "James", "initials": "J"}, {"family": "Hood", "given": "Leroy", "initials": "L"}, {"family": "Hunter", "given": "Peter", "initials": "P"}, {"family": "Jin", "given": "Li", "initials": "L"}, {"family": "Kitano", "given": "Hiroaki", "initials": "H"}, {"family": "Knoppers", "given": "Bartha", "initials": "B", "orcid": "0000-0001-7004-2722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0685488b25654257a31874181d90fd64.json"}}, {"family": "Lancet", "given": "Doron", "initials": "D"}, {"family": "Larue", "given": "Catherine", "initials": "C"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Laville", "given": "Martine", "initials": "M"}, {"family": "Lindner", "given": "Ariel B", "initials": "AB"}, {"family": "Magnan", "given": "Antoine", "initials": "A"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morin", "given": "Edgar", "initials": "E"}, {"family": "Ng", "given": "Lisa F P", "initials": "LFP"}, {"family": "Nicod", "given": "Laurent", "initials": "L"}, {"family": "Noble", "given": "Denis", "initials": "D"}, {"family": "Nottale", "given": "Laurent", "initials": "L"}, {"family": "Nowotny", "given": "Helga", "initials": "H"}, {"family": "Ochoa", "given": "Theresa", "initials": "T"}, {"family": "Okeke", "given": "Iruka N", "initials": "IN"}, {"family": "Oni", "given": "Tolu", "initials": "T"}, {"family": "Openshaw", "given": "Peter", "initials": "P", "orcid": "0000-0002-7220-2555", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ecb52d535b4a148427afc39a1e0887.json"}}, {"family": "Ozt\u00fcrk", "given": "Mehmet", "initials": "M"}, {"family": "Palkonen", "given": "Susanna", "initials": "S"}, {"family": "Paweska", "given": "Janusz T", "initials": "JT"}, {"family": "Pison", "given": "Christophe", "initials": "C"}, {"family": "Polymeropoulos", "given": "Mihael H", "initials": "MH"}, {"family": "Pristipino", "given": "Christian", "initials": "C"}, {"family": "Protzer", "given": "Ulrike", "initials": "U"}, {"family": "Roca", "given": "Josep", "initials": "J"}, {"family": "Rozman", "given": "Damjana", "initials": "D"}, {"family": "Santolini", "given": "Marc", "initials": "M", "orcid": "0000-0003-1491-0120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e4f2264a7a14e6c81da96ed42f343ba.json"}}, {"family": "Sanz", "given": "Ferran", "initials": "F", "orcid": "0000-0002-7534-7661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74a80a0137674091b2476f98498da48f.json"}}, {"family": "Scambia", "given": "Giovanni", "initials": "G"}, {"family": "Segal", "given": "Eran", "initials": "E"}, {"family": "Serageldin", "given": "Ismail", "initials": "I"}, {"family": "Soares", "given": "Marcelo Bento", "initials": "MB"}, {"family": "Sterk", "given": "Peter", "initials": "P"}, {"family": "Sugano", "given": "Sumio", "initials": "S"}, {"family": "Superti-Furga", "given": "Giulio", "initials": "G"}, {"family": "Supple", "given": "David", "initials": "D"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Urbani", "given": "Andrea", "initials": "A"}, {"family": "Valencia", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-8937-6789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80973e7b48094490adf93726d44c49b1.json"}}, {"family": "Valentini", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4637-6487", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05be585aa7984420ab85e7d779e227de.json"}}, {"family": "van der Werf", "given": "Sylvie", "initials": "S", "orcid": "0000-0002-1148-4456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a157285d7c284d92956df5befdd67e93.json"}}, {"family": "Vinciguerra", "given": "Manlio", "initials": "M"}, {"family": "Wolkenhauer", "given": "Olaf", "initials": "O"}, {"family": "Wouters", "given": "Emiel", "initials": "E"}], "type": "journal-article", "published": "2020-09-14", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "9", "pages": "1130", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.26098.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:41:39.479Z", "modified": "2026-08-20T12:41:39.864Z"}]}