{"entity": "researcher", "timestamp": "2026-08-20T20:14:02.751Z", "family": "Scheres", "given": "Sjors H W", "initials": "SHW", "orcid": "0000-0002-0462-6540", "affiliations": ["MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62"}}, "publications": [{"entity": "publication", "iuid": "e21fa31a73714586ac5e2ce2fdfa9b0b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e21fa31a73714586ac5e2ce2fdfa9b0b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e21fa31a73714586ac5e2ce2fdfa9b0b"}}, "title": "Automated model building and protein identification in cryo-EM maps.", "authors": [{"family": "Jamali", "given": "Kiarash", "initials": "K", "orcid": "0009-0008-4805-9518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2703bac619b45f68cd9b6b0e5258d13.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Zhang", "given": "Rui", "initials": "R", "orcid": "0000-0003-3159-9565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48073c47b2d04592b4a2a1090ffdc342.json"}}, {"family": "Brown", "given": "Alan", "initials": "A", "orcid": "0000-0002-0021-0476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa8915cd08984aea9b16cda6484e50b8.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Scheres", "given": "Sjors H W", "initials": "SHW", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "comparative study", "published": "2024-04-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "628", "issue": "8007", "pages": "450-457", "issn-l": "0028-0836"}, "abstract": "Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality to those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy to those built by humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will therefore remove bottlenecks and increase objectivity in cryo-EM structure determination.", "doi": "10.1038/s41586-024-07215-4", "pmid": "38408488", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11006616"}, {"db": "pii", "key": "10.1038/s41586-024-07215-4"}], "notes": [], "created": "2026-08-20T08:58:50.842Z", "modified": "2026-08-20T08:58:51.027Z"}, {"entity": "publication", "iuid": "aad8fe901d1e4010aef907a85ecd5587", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aad8fe901d1e4010aef907a85ecd5587.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aad8fe901d1e4010aef907a85ecd5587"}}, "title": "Author response: New tools for automated high-resolution cryo-EM structure determination in RELION-3", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J", "orcid": "0000-0001-8407-0759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c558645bdcb34890a1eee8786b3126d8.json"}}, {"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Hagen", "given": "Wim JH", "initials": "WJ", "orcid": "0000-0001-6229-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f90d3efecb1f420e8ba6bf2e2d5f0f91.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "peer-review", "published": "2018-11-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.42166.030", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:52:40.740Z", "modified": "2026-08-20T13:52:40.775Z"}, {"entity": "publication", "iuid": "9c4cbb326ac4478cbf8526a0eee0ca4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c4cbb326ac4478cbf8526a0eee0ca4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c4cbb326ac4478cbf8526a0eee0ca4d"}}, "title": "RELION-3: new tools for automated high-resolution cryo-EM structure determination", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J", "orcid": "0000-0001-8407-0759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c558645bdcb34890a1eee8786b3126d8.json"}}, {"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ea51bfa66d48b7a43559c3d0eaa59f.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Hagen", "given": "Wim J H", "initials": "WJH", "orcid": "0000-0001-6229-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f90d3efecb1f420e8ba6bf2e2d5f0f91.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors H W", "initials": "SHW", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "posted-content", "published": "2018-09-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/421123", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:09.289Z", "modified": "2026-08-20T11:11:09.486Z"}, {"entity": "publication", "iuid": "36ab7066bca44b7086ed20e964ffc62e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36ab7066bca44b7086ed20e964ffc62e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36ab7066bca44b7086ed20e964ffc62e"}}, "title": "Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.", "authors": [{"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors Hw", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "journal article", "published": "2018-06-01", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "7", "issue": null, "issn-l": "2050-084X"}, "abstract": "Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.", "doi": "10.7554/eLife.36861", "pmid": "29856314", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC6005684"}, {"db": "pii", "key": "36861"}], "notes": [], "created": "2019-01-17T13:50:40.156Z", "modified": "2026-08-20T13:52:32.948Z"}, {"entity": "publication", "iuid": "984de887bf7b4ea28b6456fcb664dd47", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/984de887bf7b4ea28b6456fcb664dd47.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/984de887bf7b4ea28b6456fcb664dd47"}}, "title": "Author response: Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION", "authors": [{"family": "Nakane", "given": "Takanori", "initials": "T", "orcid": "0000-0003-2697-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fa28db5ed51428f85508b6986fa0f72.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a3803ee817a464ca07c849c07096dc2.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}], "type": "peer-review", "published": "2018-05-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.36861.022", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:52:34.711Z", "modified": "2026-08-20T13:52:34.747Z"}, {"entity": "publication", "iuid": "3e3db83f40c04049bf6258cd7aafb9a0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3db83f40c04049bf6258cd7aafb9a0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3db83f40c04049bf6258cd7aafb9a0"}}, "title": "Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.", "authors": [{"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Scheres", "given": "Sjors Hw", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "journal article", "published": "2016-11-15", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "5", "issue": null, "issn-l": "2050-084X"}, "abstract": "By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.", "doi": "10.7554/eLife.18722", "pmid": "27845625", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC5310839"}, {"db": "pii", "key": "e18722"}], "notes": [], "created": "2018-12-05T08:35:33.055Z", "modified": "2026-08-20T13:51:49.664Z"}, {"entity": "publication", "iuid": "3f65caaf36df4efa949a725983b14502", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f65caaf36df4efa949a725983b14502.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f65caaf36df4efa949a725983b14502"}}, "title": "Author response: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2", "authors": [{"family": "Kimanius", "given": "Dari", "initials": "D"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO"}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH", "orcid": "0000-0002-0462-6540", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b64851b999fd42f7bf7b25856946dc62.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "peer-review", "published": "2016-10-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.18722.024", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:51:51.527Z", "modified": "2026-08-20T13:51:51.577Z"}]}