{"entity": "researcher", "timestamp": "2026-08-20T21:24:02.595Z", "family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "affiliations": ["Science for Life Laboratory, 172 21, Solna, Sweden.", "Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706"}}, "publications": [{"entity": "publication", "iuid": "740fdf09151b47df8a5af5bad9c8be82", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/740fdf09151b47df8a5af5bad9c8be82.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/740fdf09151b47df8a5af5bad9c8be82"}}, "title": "M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.", "authors": [{"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Kalakoti", "given": "Yogesh", "initials": "Y"}, {"family": "Sundar", "given": "Durai", "initials": "D", "orcid": "0000-0002-6549-6663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bf8c45f2b9848f2861604fac7f8613c.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": "2024-01-02", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "1", "issn-l": "1367-4803"}, "abstract": "Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the pLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal binding.\n\nOn independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall = 84.6%) in distinguishing metal binding from non-binding proteins compared to AUROC of 0.74 (recall = 61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e. Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the pLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties.\n\nM-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). The GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.", "doi": "10.1093/bioinformatics/btad782", "pmid": "38175787", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10792727"}, {"db": "pii", "key": "7510839"}], "notes": [], "created": "2026-08-20T09:39:49.393Z", "modified": "2026-08-20T09:39:49.502Z"}, {"entity": "publication", "iuid": "1a559ed2dafd466d8e52c3a17f62d0f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a559ed2dafd466d8e52c3a17f62d0f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a559ed2dafd466d8e52c3a17f62d0f5"}}, "title": "The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems.", "authors": [{"family": "Ernits", "given": "Karin", "initials": "K"}, {"family": "Saha", "given": "Chayan Kumar", "initials": "CK", "orcid": "0000-0002-5357-517X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3d0b705fbd94f5a82d2825b0f7d40cb.json"}}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T"}, {"family": "Chouhan", "given": "Bhanu", "initials": "B"}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Buttress", "given": "Jessica A", "initials": "JA", "orcid": "0000-0001-8822-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f7cee57e9d94c53b46aed566af418e7.json"}}, {"family": "Duque-Pedraza", "given": "Juli\u00e1n J", "initials": "JJ"}, {"family": "Bojar", "given": "Veda", "initials": "V"}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA"}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.json"}}, {"family": "Johansson", "given": "Marcus J O", "initials": "MJO", "orcid": "0000-0001-7117-7426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16.json"}}, {"family": "Mets", "given": "Toomas", "initials": "T", "orcid": "0000-0002-6796-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbceebe30234575b3575ef4f44c0511.json"}}, {"family": "Rustamova", "given": "Aytan", "initials": "A"}, {"family": "D\u017eigurski", "given": "Jelisaveta", "initials": "J", "orcid": "0000-0003-2885-6241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ff5ff6b4a5a4b3ba1f08f4d34440d4c.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A"}, {"family": "Strahl", "given": "Henrik", "initials": "H", "orcid": "0000-0003-4416-2178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17b2bf7837f7474dac625be9421a223e.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "33", "pages": "e2305393120", "issn-l": "0027-8424"}, "abstract": "Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins), we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralization by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralizing mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralization, while in multidomain antitoxins the neutralization is mediated by other domains, such as PAD1, Phd-C, and ZFD. We hypothesize that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 NetFlax TA systems and used domain annotations and metabolic labeling assays to predict their potential mechanisms of toxicity (such as membrane disruption, and inhibition of cell division or protein synthesis) as well as biological functions (such as antiphage defense). We have validated the antiphage activity of a RosmerTA system encoded by Gordonia phage Kita, and used fluorescence microscopy to confirm its predicted membrane-depolarizing activity. The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.", "doi": "10.1073/pnas.2305393120", "pmid": "37556498", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10440598"}], "notes": [], "created": "2026-08-20T09:31:27.979Z", "modified": "2026-08-20T09:31:28.324Z"}, {"entity": "publication", "iuid": "07548c23bc5e48ab8a2cb5f1cd9a4a65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07548c23bc5e48ab8a2cb5f1cd9a4a65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07548c23bc5e48ab8a2cb5f1cd9a4a65"}}, "title": "Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.", "authors": [{"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": "2023-07-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "39", "issue": "7", "issn-l": "1367-4803"}, "abstract": "Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.\n\nWe analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g. TM-score) but poorly on another (e.g. DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.\n\nAll scripts, models, and data used to perform the analysis in this study are freely available at https://gitlab.com/ElofssonLab/afm-benchmark.", "doi": "10.1093/bioinformatics/btad424", "pmid": "37405868", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10348836"}, {"db": "pii", "key": "7219714"}], "notes": [], "created": "2026-08-20T09:39:38.444Z", "modified": "2026-08-20T09:39:38.475Z"}, {"entity": "publication", "iuid": "528de81a6f214d86a9366806efd87b77", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/528de81a6f214d86a9366806efd87b77.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/528de81a6f214d86a9366806efd87b77"}}, "title": "The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems", "authors": [{"family": "Ernits", "given": "Karin", "initials": "K", "orcid": "0000-0003-1072-4945", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f3dbd4a451c45878f71cb0b441c561d.json"}}, {"family": "Saha", "given": "Chayan Kumar", "initials": "CK", "orcid": "0000-0002-5357-517X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3d0b705fbd94f5a82d2825b0f7d40cb.json"}}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T", "orcid": "0000-0002-2591-9588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8747a493473b4ebcabf9b1847be69e29.json"}}, {"family": "Chouhan", "given": "Bhanu", "initials": "B", "orcid": "0000-0002-3918-5925", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68a24320b5684139a54e7700443360ac.json"}}, {"family": "Shenoy", "given": "Aditi", "initials": "A", "orcid": "0000-0001-7748-2501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35bef00b985a45d59602675316e3d706.json"}}, {"family": "Duque-Pedraza", "given": "Julian J", "initials": "JJ", "orcid": "0009-0008-6943-2967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/726403acf6a14088b5a3f48ecda03004.json"}}, {"family": "Bojar", "given": "Veda", "initials": "V", "orcid": "0009-0009-0321-143X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7668b4f044fe689251d5bab9edf60.json"}}, {"family": "Nakamoto", "given": "Jose A", "initials": "JA", "orcid": "0000-0001-8312-433X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/590d08398d614e9ca3307803cd263b8d.json"}}, {"family": "Kurata", "given": "Tatsuaki", "initials": "T", "orcid": "0000-0001-5986-7141", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3ed90eb741422db2af62827e8947e2.json"}}, {"family": "Egorov", "given": "Artyom", "initials": "A", "orcid": "0000-0001-5578-5384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db620b86e13e45618e7cad6a06cd474e.json"}}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.json"}}, {"family": "Johansson", "given": "Marcus J O", "initials": "MJO", "orcid": "0000-0001-7117-7426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ee1c60ebb934dfd996e67a32790db16.json"}}, {"family": "Mets", "given": "Toomas", "initials": "T", "orcid": "0000-0002-6796-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbceebe30234575b3575ef4f44c0511.json"}}, {"family": "Rustamova", "given": "Aytan", "initials": "A", "orcid": "0009-0005-5964-3179", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf2a2d0e8ab349dea52a8ebf0f4285ee.json"}}, {"family": "Dzigurski", "given": "Jelisaveta", "initials": "J", "orcid": "0000-0003-2885-6241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ff5ff6b4a5a4b3ba1f08f4d34440d4c.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A", "orcid": "0000-0002-6280-1714", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cbbb1848368486e803f0236d9127c06.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Atkinson", "given": "Gemma Catherine", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "posted-content", "published": "2023-03-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.03.22.533649", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:44:41.759Z", "modified": "2026-08-20T10:44:42.195Z"}, {"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": "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": "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": "https://publications-affiliated.scilifelab.se/researcher/48d94181fa7444358e4c67b2e5e4c8b0.json"}}, {"family": "\u00c1cs", "given": "Veronika", "initials": "V", "orcid": "0000-0001-6260-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69aa57bb7fc040da970f8e5deb9cb899.json"}}, {"family": "Farahi", "given": 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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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"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": "ac4436481a8e4c5fa3c6f8589d010029", "links": {"self": {"href": 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