{"entity": "researcher", "timestamp": "2026-08-20T21:26:43.555Z", "family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "affiliations": ["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e"}}, "publications": [{"entity": "publication", "iuid": "7a190019b7f04814bc65ca0fb5f89942", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a190019b7f04814bc65ca0fb5f89942.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a190019b7f04814bc65ca0fb5f89942"}}, "title": "Towards a structurally resolved human protein interaction network.", "authors": [{"family": "Burke", "given": "David F", "initials": "DF", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.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": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1668-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James E", "initials": "JE", "orcid": "0000-0001-6441-6089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66c3622f73ef4c62a4100d87ab6aeded.json"}}, {"family": "Leitner", "given": "Alexander", "initials": "A", "orcid": "0000-0003-4126-0725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca32a3af642745ea9d26f0e7f1413b6a.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "30", "issue": "2", "pages": "216-225", "issn-l": "1545-9985"}, "abstract": "Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their molecular mechanisms. However, fewer than 5% of hundreds of thousands of human protein interactions have been structurally characterized. Here we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human protein interactions. We show that experiments can orthogonally confirm higher-confidence models. We identify 3,137 high-confidence models, of which 1,371 have no homology to a known structure. We identify interface residues harboring disease mutations, suggesting potential mechanisms for pathogenic variants. Groups of interface phosphorylation sites show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple protein interactions as signaling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies helping to expand our understanding of human cell biology.", "doi": "10.1038/s41594-022-00910-8", "pmid": "36690744", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9935395"}, {"db": "pii", "key": "10.1038/s41594-022-00910-8"}], "notes": [], "created": "2026-08-20T09:03:53.064Z", "modified": "2026-08-20T09:03:53.359Z"}, {"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": "ce33baa2344a46f2a266278abbc3541e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce33baa2344a46f2a266278abbc3541e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce33baa2344a46f2a266278abbc3541e"}}, "title": "Towards a structurally resolved human protein interaction network", "authors": [{"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Burke", "given": "David", "initials": "D", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.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": "Dunham", "given": "Alistair", "initials": "A"}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard", "initials": "R", "orcid": "0000-0002-1668-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James", "initials": "J", "orcid": "0000-0001-6441-6089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66c3622f73ef4c62a4100d87ab6aeded.json"}}, {"family": "Leitner", "given": "Alexander", "initials": "A", "orcid": "0000-0003-4126-0725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca32a3af642745ea9d26f0e7f1413b6a.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"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": "2021-12-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1098605/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:57:59.578Z", "modified": "2026-08-20T12:57:59.681Z"}, {"entity": "publication", "iuid": "1be1bcb2fb5a44e4b1c129f2af52fc32", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1be1bcb2fb5a44e4b1c129f2af52fc32.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1be1bcb2fb5a44e4b1c129f2af52fc32"}}, "title": "Towards a structurally resolved human protein interaction network", "authors": [{"family": "Burke", "given": "David F", "initials": "DF", "orcid": "0000-0001-8830-3951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ae9a94abf5e47778d59e4f3c9d8e62e.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Barrio-Hernandez", "given": "Inigo", "initials": "I", "orcid": "0000-0002-5686-0451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59ccf621e75c48868e9c215b04dcf787.json"}}, {"family": "Memon", "given": "Danish", "initials": "D", "orcid": "0000-0002-1365-0710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9e1ae20abe4f7f94af1f6856d026bc.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"}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Dunham", "given": "Alistair S", "initials": "AS", "orcid": "0000-0001-9076-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41348047cf374b149851ea1b9bca2014.json"}}, {"family": "Albanese", "given": "Pascal", "initials": "P"}, {"family": "Keller", "given": "Andrew", "initials": "A"}, {"family": "Scheltema", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1668-0253", "researcher": {"href": 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