{"entity": "researcher", "timestamp": "2026-08-20T21:26:39.177Z", "family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "affiliations": ["Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9"}}, "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": "742f8e9ffe22495b83683c9efa073fe8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/742f8e9ffe22495b83683c9efa073fe8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/742f8e9ffe22495b83683c9efa073fe8"}}, "title": "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}, {"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": "2022-10-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6028", "issn-l": "2041-1723"}, "abstract": "AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. Here we show that one can predict the structure of large complexes starting from predictions of subcomponents. We assemble 91 out of 175 complexes with 10-30 chains from predicted subcomponents using Monte Carlo tree search, with a median TM-score of 0.51. There are 30 highly accurate complexes (TM-score \u22650.8, 33% of complete assemblies). We create a scoring function, mpDockQ, that can distinguish if assemblies are complete and predict their accuracy. We find that complexes containing symmetry are accurately assembled, while asymmetrical complexes remain challenging. The method is freely available and accesible as a Colab notebook https://colab.research.google.com/github/patrickbryant1/MoLPC/blob/master/MoLPC.ipynb .", "doi": "10.1038/s41467-022-33729-4", "pmid": "36224222", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9556563"}, {"db": "pii", "key": "10.1038/s41467-022-33729-4"}], "notes": [], "created": "2026-08-20T08:52:21.196Z", "modified": "2026-08-20T08:52:21.329Z"}, {"entity": "publication", "iuid": "fe628affc8944824b57b88e27c29539f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe628affc8944824b57b88e27c29539f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe628affc8944824b57b88e27c29539f"}}, "title": "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.", "authors": [{"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Zhu", "given": "Wensi", "initials": "W"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P"}], "type": "posted-content", "published": "2022-07-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1870813/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:58:17.863Z", "modified": "2026-08-20T12:58:17.931Z"}, {"entity": "publication", "iuid": "f467354e0e524232a2662b7209c194ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f467354e0e524232a2662b7209c194ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f467354e0e524232a2662b7209c194ba"}}, "title": "Scoring of protein-protein docking models utilizing predicted interface residues.", "authors": [{"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.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": "2022-07-00", "journal": {"title": "Proteins", "issn": "1097-0134", "volume": "90", "issue": "7", "pages": "1493-1505", "issn-l": "0887-3585"}, "abstract": "Scoring docking solutions is a difficult task, and many methods have been developed for this purpose. In docking, only a handful of the hundreds of thousands of models generated by docking algorithms are acceptable, causing difficulties when developing scoring functions. Today's best scoring functions can significantly increase the number of top-ranked models but still fail for most targets. Here, we examine the possibility of utilizing predicted interface residues to score docking models generated during the scan stage of a docking algorithm. Many methods have been developed to infer the regions of a protein surface that interact with another protein, but most have not been benchmarked using docking algorithms. This study systematically tests different interface prediction methods for scoring >300.000 low-resolution rigid-body template free docking decoys. Overall we find that contact-based interface prediction by BIPSPI is the best method to score docking solutions, with >12% of first ranked docking models being acceptable. Additional experiments indicated precision as a high-importance metric when estimating interface prediction quality, focusing on docking constraints production. Finally, we discussed several limitations for adopting interface predictions as constraints in a docking protocol.", "doi": "10.1002/prot.26330", "pmid": "35246997", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9314140"}], "notes": [], "created": "2026-08-20T06:35:20.680Z", "modified": "2026-08-20T06:35:20.817Z"}, {"entity": "publication", "iuid": "abe0fcfa5eca477384d4348b12aa56a3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abe0fcfa5eca477384d4348b12aa56a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abe0fcfa5eca477384d4348b12aa56a3"}}, "title": "Author Correction: Improved prediction of protein-protein interactions using AlphaFold2.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "published erratum", "published": "2022-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1694", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-022-29480-5", "pmid": "35332153", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8948285"}, {"db": "pii", "key": "10.1038/s41467-022-29480-5"}], "notes": [], "created": "2026-08-20T08:51:54.323Z", "modified": "2026-08-20T08:51:54.409Z"}, {"entity": "publication", "iuid": "1dfa3174fd1847d4b909d3625bcedb14", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dfa3174fd1847d4b909d3625bcedb14.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dfa3174fd1847d4b909d3625bcedb14"}}, "title": "Improved prediction of protein-protein interactions using AlphaFold2.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Pozzati", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4303-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94129216debe4e22ab3f3b74c33f9ab9.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": "2022-03-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1265", "issn-l": "2041-1723"}, "abstract": "Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ \u2265 0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR.", "doi": "10.1038/s41467-022-28865-w", "pmid": "35273146", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8913741"}, {"db": "pii", "key": "10.1038/s41467-022-28865-w"}], "notes": [], "created": "2026-08-20T08:51:52.439Z", "modified": "2026-08-20T08:51:52.517Z"}, {"entity": "publication", "iuid": "ecddf63436744689a1ed09649fa2610a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ecddf63436744689a1ed09649fa2610a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ecddf63436744689a1ed09649fa2610a"}}, "title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.", "authors": [{"family": "Quaglia", "given": "Federica", "initials": "F", "orcid": "0000-0002-0341-4888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6657e12ee16a450aaca2c23b04e5a283.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": "Salladini", "given": "Edoardo", "initials": "E", "orcid": "0000-0002-5152-5953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35587acab31f476eafa5885746e56477.json"}}, {"family": "Hatos", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0001-9224-9820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c092bf996e3f4583835c054ab625bd82.json"}}, {"family": "Pancsa", "given": "Rita", "initials": "R", "orcid": "0000-0003-0849-9312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be46edae0a264d77be41af470f1d8329.json"}}, {"family": "Chemes", "given": "Luc\u00eda B", "initials": "LB", "orcid": "0000-0003-0192-9906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a33ae695d0143598c079e0c05a4e849.json"}}, {"family": "Pajkos", "given": "M\u00e1ty\u00e1s", "initials": "M", "orcid": "0000-0001-5791-9825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ac7745fffdb449eb928187f60a643c8.json"}}, {"family": "Lazar", "given": "Tamas", "initials": "T", "orcid": "0000-0001-7496-6711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2569bcb52a954ba4a4cac2094c455a67.json"}}, {"family": "Pe\u00f1a-D\u00edaz", "given": "Samuel", "initials": "S", "orcid": "0000-0002-2902-823X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b3893fbe1094949ba567118a7bfa147.json"}}, {"family": "Santos", "given": "Jaime", "initials": "J", "orcid": "0000-0001-9045-7765", "researcher": {"href": 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"given": "Eva", "initials": "E", "orcid": "0000-0002-3006-2910", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9351f3e947da424d8e20ad68127d8413.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Szaniszl\u00f3", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0002-3130-9284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2610135fd9b347229c2280fa5527d73c.json"}}, {"family": "Tsirigos", "given": "Konstantinos D", "initials": "KD", "orcid": "0000-0001-5280-1107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85e1896a52d04cb7b4475ebba4d17505.json"}}, {"family": "Veljkovic", "given": "Nevena", "initials": "N", "orcid": "0000-0001-6562-5800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a1d0994c8fb42c5abf35b0e82884c18.json"}}, {"family": "Parisi", "given": "Gustavo", "initials": "G", "orcid": "0000-0001-7444-1624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014eb4c06cbe4597ad14afc5f9146f6a.json"}}, {"family": "Ventura", "given": "Salvador", "initials": "S", "orcid": "0000-0002-9652-6351", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e0afcd4cf084de6be1e2e606f6e954c.json"}}, {"family": "Doszt\u00e1nyi", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-3624-5937", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77615a3783aa490ebc0dc300958ea70f.json"}}, {"family": "Tompa", "given": "Peter", "initials": "P", "orcid": "0000-0001-8042-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57f930a048ce4e5b9d65c9d173bd9954.json"}}, {"family": "Tosatto", "given": "Silvio C E", "initials": "SCE", "orcid": "0000-0003-4525-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/152b8eca864e44f1954ee4952c60aa0d.json"}}, {"family": "Piovesan", "given": "Damiano", "initials": "D", "orcid": "0000-0001-8210-2390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/994db11834b0446895c5cd4b28be1d8b.json"}}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "50", "issue": "D1", "pages": "D480-D487", "issn-l": "0305-1048"}, "abstract": "The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.", "doi": "10.1093/nar/gkab1082", "pmid": "34850135", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8728214"}, {"db": "pii", "key": "6439667"}], "notes": [], "created": "2026-08-20T09:49:35.446Z", "modified": "2026-08-20T09:49:37.565Z"}, {"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", 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