{"entity": "researcher", "timestamp": "2026-08-20T21:14:51.541Z", "family": "Kundrotas", "given": "Petras", "initials": "P", "orcid": "0000-0001-5080-1664", "affiliations": ["Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden.", "Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e645003f2000464c9e289ccd3b92ce68"}}, "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": "3fe115a522b44ef39a21a3616e793f66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3fe115a522b44ef39a21a3616e793f66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3fe115a522b44ef39a21a3616e793f66"}}, "title": "Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes", "authors": [{"family": "Zhu", "given": "Wensi", "initials": "W", "orcid": "0000-0002-5032-3727", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28ff85e976a54cd88252d8c5b6447de1.json"}}, {"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", "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": "posted-content", "published": "2022-12-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.08.519586", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:42:52.594Z", "modified": "2026-08-20T10:42:52.690Z"}, {"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": "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": "https://publications-affiliated.scilifelab.se/researcher/de6c6b9b87574d7eb67d48a73ab5f230.json"}}, {"family": "Bruce", "given": "James E", "initials": "JE"}, {"family": "Leitner", "given": "Alexander", "initials": "A"}, {"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": "posted-content", "published": "2021-11-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.11.08.467664", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:07:27.911Z", "modified": "2026-08-20T10:07:27.979Z"}, {"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"}, {"entity": "publication", "iuid": "d2817ef2febd446a9cb152e3b1c5f5ca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2817ef2febd446a9cb152e3b1c5f5ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2817ef2febd446a9cb152e3b1c5f5ca"}}, "title": "Improved protein docking by predicted interface residues", "authors": [{"family": "Pozzati", "given": "Gabriele", "initials": "G"}, {"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": "posted-content", "published": "2021-08-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.08.25.457642", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:06:29.465Z", "modified": "2026-08-20T10:06:29.527Z"}]}