{"entity": "researcher", "timestamp": "2026-07-17T08:40:02.655Z", "family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5"}}, "publications": [{"entity": "publication", "iuid": "6dfc892282ff426f998cbc7c26e3828f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dfc892282ff426f998cbc7c26e3828f"}}, "title": "The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A.", "authors": [{"family": "Hultman", "given": "Johanna", "initials": "J", "orcid": "0009-0000-8066-228X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd75d9341822427db7b8b8b8510123fd.json"}}, {"family": "Morad", "given": "Vivian", "initials": "V", "orcid": "0000-0001-9665-4532", "researcher": {"href": "https://publications.scilifelab.se/researcher/36505a4d209d4f439785a062205b180c.json"}}, {"family": "Tanner", "given": "Eliane", "initials": "E"}, {"family": "Kenney", "given": "Tristan M G", "initials": "TMG", "orcid": "0000-0001-8242-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/b739b627992645428ea12ed180dab914.json"}}, {"family": "Pietras", "given": "Zuzanna", "initials": "Z", "orcid": "0000-0002-4501-7311", "researcher": {"href": "https://publications.scilifelab.se/researcher/973d7a63037c432db0f7ca9607b8525b.json"}}, {"family": "Khare", "given": "Lalit Pramod", "initials": "LP"}, {"family": "Derbyshire", "given": "Dean", "initials": "D"}, {"family": "Resetca", "given": "Diana", "initials": "D"}, {"family": "Arrowsmith", "given": "Cheryl H", "initials": "CH"}, {"family": "Aili", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7001-9415", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc760610215a4dee9061f28723b97e62.json"}}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S", "orcid": "0000-0002-7694-285X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6416b323664f4126b70067193d7b8347.json"}}, {"family": "Penn", "given": "Linda Z", "initials": "LZ", "orcid": "0000-0001-8133-5459", "researcher": {"href": "https://publications.scilifelab.se/researcher/780529b33355480890244ff1039ea64f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Ahlner", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-7004-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/08cd17a1108045b5be32cd492a082453.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M", "orcid": "0000-0002-0492-5890", "researcher": {"href": "https://publications.scilifelab.se/researcher/3caade7942f84928b12656cb7e5f8493.json"}}], "type": "journal article", "published": "2026-02-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The intrinsically disordered MYC proteins are master regulators of cellular growth and function, but when deregulated they become cancer drivers. MYC-protein interactions are key to oncogenesis, and while disrupting such interactions would be of significant therapeutic benefit, the intrinsically disordered properties of MYC have dramatically hampered their characterization. Here, we apply an integrated structural biology approach to describe the structure and dynamics of the N-Myc-Aurora A complex, which is critical in neuroendocrine tumor progression. We reveal a functional interaction where multiple binding sites on N-Myc interact with the Aurora A N-lobe. The interaction is governed by aromatic clusters within the conserved MB0 and MBI motifs in N-Myc that interact with Aurora A in a dynamic binding mode that allosterically promotes kinase activation. We show that N-Myc binding to the Aurora A N-lobe can be inhibited by the small-molecule AurkinA, providing opportunity for therapeutical strategies to disrupt this interaction.", "doi": "10.1038/s41467-026-69725-1", "pmid": "41735282", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12936163"}, {"db": "pii", "key": "10.1038/s41467-026-69725-1"}], "notes": [], "created": "2026-04-07T14:24:57.298Z", "modified": "2026-04-07T14:24:58.191Z"}, {"entity": "publication", "iuid": "aa929085914c406a86ecd4074e8e28b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa929085914c406a86ecd4074e8e28b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa929085914c406a86ecd4074e8e28b5"}}, "title": "MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling.", "authors": [{"family": "Raouraoua", "given": "Nessim", "initials": "N", "orcid": "0009-0005-5652-684X", "researcher": {"href": "https://publications.scilifelab.se/researcher/95499cc13f5f4ff8b5e688b88d99bbb0.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "V\u00e9ry", "given": "Thibaut", "initials": "T"}, {"family": "Blanchet", "given": "Christophe", "initials": "C"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Lensink", "given": "Marc F", "initials": "MF", "orcid": "0000-0003-3957-9470", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f27d0f7d8b407dbc9a8fdd13622248.json"}}, {"family": "Brysbaert", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-6807-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/74499da411614b84bea0d7c8986cd27e.json"}}], "type": "journal article", "published": "2024-11-11", "journal": {"title": "Nat Comput Sci", "issn": "2662-8457", "issn-l": null}, "abstract": "Massive sampling in AlphaFold enables access to increased structural diversity. In combination with its efficient confidence ranking, this unlocks elevated modeling capabilities for monomeric structures and foremost for protein assemblies. However, the approach struggles with GPU cost and data storage. Here we introduce MassiveFold, an optimized and customizable version of AlphaFold that runs predictions in parallel, reducing the computing time from several months to hours. MassiveFold is scalable and able to run on anything from a single computer to a large GPU infrastructure, where it can fully benefit from all the computing nodes.", "doi": "10.1038/s43588-024-00714-4", "pmid": "39528570", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s43588-024-00714-4"}], "notes": [], "created": "2024-11-18T22:11:25.912Z", "modified": "2024-11-18T22:11:28.574Z"}, {"entity": "publication", "iuid": "db72b1430ff149429d4ed6274c089a9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db72b1430ff149429d4ed6274c089a9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db72b1430ff149429d4ed6274c089a9b"}}, "title": "Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.", "authors": [{"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Azinas", "given": "Stavros", "initials": "S", "orcid": "0000-0002-3744-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ec0cb5b5df4b4f89780ce3a08efc89.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}], "type": "journal article", "published": "2024-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8724", "issn-l": "2041-1723"}, "abstract": "Since the release of AlphaFold, researchers have actively refined its predictions and attempted to integrate it into existing pipelines for determining protein structures. These efforts have introduced a number of functionalities and optimisations at the latest Critical Assessment of protein Structure Prediction edition (CASP15), resulting in a marked improvement in the prediction of multimeric protein structures. However, AlphaFold's capability of predicting large protein complexes is still limited and integrating experimental data in the prediction pipeline is not straightforward. In this study, we introduce AF_unmasked to overcome these limitations. Our results demonstrate that AF_unmasked can integrate experimental information to build larger or hard to predict protein assemblies with high confidence. The resulting predictions can help interpret and augment experimental data. This approach generates high quality (DockQ score > 0.8) structures even when little to no evolutionary information is available and imperfect experimental structures are used as a starting point. AF_unmasked is developed and optimised to fill incomplete experimental structures (structural inpainting), which may provide insights into protein dynamics. In summary, AF_unmasked provides an easy-to-use method that efficiently integrates experiments to predict large protein complexes more confidently.", "doi": "10.1038/s41467-024-52951-w", "pmid": "39379372", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Cryo-EM": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11461844"}, {"db": "pii", "key": "10.1038/s41467-024-52951-w"}], "notes": [], "created": "2024-11-08T10:09:12.989Z", "modified": "2024-11-15T15:09:44.609Z"}, {"entity": "publication", "iuid": "97518e7e5db049da9b688c32f3c81ac7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97518e7e5db049da9b688c32f3c81ac7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97518e7e5db049da9b688c32f3c81ac7"}}, "title": "DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.", "authors": [{"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}], "type": "journal article", "published": "2024-10-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "10", "issn-l": "1367-4803"}, "abstract": "It is important to assess the quality of modeled biomolecules to benchmark and assess the performance of different prediction methods. DockQ has emerged as the standard tool for assessing the quality of protein interfaces in model structures against given references. However, as predictions of large multimers with multiple chains become more common, DockQ needs to be updated with more functionality for robustness and speed. Moreover, as the field progresses and more methods are released to predict interactions between proteins and other types of molecules, such as nucleic acids and small molecules, it becomes necessary to have a tool that can assess all types of interactions.\n\nHere, we present a complete reimplementation of DockQ in pure Python. The updated version of DockQ is more portable, faster and introduces novel functionalities, such as automatic DockQ calculations for multiple interfaces and automatic chain mapping with multi-threading. These enhancements are designed to facilitate comparative analyses of protein complexes, particularly large multi-chain complexes. Furthermore, DockQ is now also able to score interfaces between proteins, nucleic acids, and small molecules.\n\nDockQ v2 is available online at: https://wallnerlab.org/DockQ.", "doi": "10.1093/bioinformatics/btae586", "pmid": "39348158", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11467047"}, {"db": "pii", "key": "7796530"}], "notes": [], "created": "2024-11-08T10:09:15.641Z", "modified": "2024-11-08T10:09:15.788Z"}, {"entity": "publication", "iuid": "f6952d433d3d4a739c73bcfe7118c1ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae"}}, "title": "Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.", "authors": [{"family": "Wallerstein", "given": "Johan", "initials": "J"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Levkovets", "given": "Maria", "initials": "M", "orcid": "0000-0002-1805-9057", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf8cc61d91474483ab51728701d2f75a.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Malmodin", "given": "Daniel", "initials": "D"}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}], "type": "journal article", "published": "2024-07-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "868", "issn-l": "2399-3642"}, "abstract": "Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme.", "doi": "10.1038/s42003-024-06558-y", "pmid": "39014105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development", "Swedish NMR Centre": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11252132"}, {"db": "pii", "key": "10.1038/s42003-024-06558-y"}], "notes": [], "created": "2024-08-06T09:19:26.577Z", "modified": "2025-10-17T13:03:52.905Z"}]}