{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:14:16Z","timestamp":1772118856712,"version":"3.50.1"},"reference-count":45,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2025,7,28]],"date-time":"2025-07-28T00:00:00Z","timestamp":1753660800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P41 GM109824"],"award-info":[{"award-number":["P41 GM109824"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM083960"],"award-info":[{"award-number":["R01 GM083960"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2025,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Building an accurate atomic structure model of a protein into a cryo\u2010electron microscopy (cryo\u2010EM) map at worse than 3\u2009\u00c5 resolution is difficult. To facilitate this task, we devised a method for assigning the amino acid residue sequence to the backbone fragments traced in an input cryo\u2010EM map (\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    ).\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    relies on a Bayesian scoring function for ranking 20 standard amino acid residue types at a given backbone position, based on the fit to a density map, map resolution, and secondary structure propensity. The fit to a density is quantified by a convolutional neural network that was trained on ~5.56 million amino acid residue densities extracted from cryo\u2010EM maps at 3\u201310\u2009\u00c5 resolution and corresponding atomic structure models deposited in the Electron Microscopy Data Bank (EMDB). We benchmarked\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    by predicting the sequences of 58,044 distinct \u0251\u2010helix and \u03b2\u2010strand fragments, given the fragment backbone coordinates fitted in their density maps.\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    identifies the correct sequence as the best\u2010scoring sequence in 77.8% of these cases. We also assessed\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    on separate datasets of cryo\u2010EM maps at resolutions from 4 to 6\u2009\u00c5. The accuracy of\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    (58%) was better than that of three tested state\u2010of\u2010the\u2010art methods, including\n                    <jats:italic>findMysequence<\/jats:italic>\n                    (45%), ModelAngelo (27%), and\n                    <jats:italic>sequence_from_map<\/jats:italic>\n                    in\n                    <jats:italic>Phenix<\/jats:italic>\n                    (12.9%). We further illustrate\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    by threading the Severe Acute Respiratory Syndrome Coronavirus 2 Non\u2010Structural Protein 2 sequence into eight cryo\u2010EM maps at resolutions from 3.7 to 7.0\u2009\u00c5.\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    is implemented in our open\u2010source\n                    <jats:italic>Integrative Modeling Platform<\/jats:italic>\n                    (IMP) program. Thus, it is expected to be helpful for integrative structure modeling based on a cryo\u2010EM map and other information, such as models of protein complex components and chemical crosslinks between them.\n                    <jats:italic>EMSequenceFinder<\/jats:italic>\n                    is available as part of our open\u2010source IMP distribution at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/integrativemodeling.org\/\">https:\/\/integrativemodeling.org\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1002\/pro.70217","type":"journal-article","created":{"date-parts":[[2025,7,28]],"date-time":"2025-07-28T13:09:09Z","timestamp":1753708149000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Recognizing amino acid sidechains in a medium\u2010resolution cryo\u2010electron density map"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5047-6985","authenticated-orcid":false,"given":"Dibyendu","family":"Mondal","sequence":"first","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vipul","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tadej","family":"Satler","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"},{"name":"Department of Synthetic Biology and Immunology National Institute of Chemistry  Ljubljana Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rakesh","family":"Ramachandran","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Saltzberg","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilan","family":"Chemmama","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kala Bharath","family":"Pilla","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ignacia","family":"Echeverria","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Pharmacology University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin M.","family":"Webb","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7432-3211","authenticated-orcid":false,"given":"Meghna","family":"Gupta","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Klim","family":"Verba","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Pharmacology University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0435-6197","authenticated-orcid":false,"given":"Andrej","family":"Sali","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences University of California, San Francisco  San Francisco California USA"},{"name":"Department of Pharmaceutical Chemistry University of California, San Francisco  San Francisco California USA"},{"name":"Quantitative Biosciences Institute, University of California, San Francisco  San Francisco California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,7,28]]},"reference":[{"key":"e_1_2_8_2_1","unstructured":"AbadiM BarhamP ChenJ ChenZ DavisA DeanJ et al.TensorFlow. 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