{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T18:51:26Z","timestamp":1789411886727,"version":"build-2803163510"},"reference-count":37,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM100482"],"award-info":[{"award-number":["R01GM100482"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Since CASP13, experimentalists have been encouraged to provide their cryo\u2010EM data along with the derived atomic models to the CASP organizers to aid assessment. In CASP16, 38 cryo\u2010EM datasets were provided for assessment, which represented most cryo\u2010EM targets. The corresponding targets typically comprised a single derived atomic structure; however, that model may be only one of several valid conformations. Flexibility often manifests as low\u2010resolution regions in a cryo\u2010EM reconstruction, particularly in RNA but often also in protein complexes. We show that local resolution in the reconstruction correlates well with the root\u2010mean\u2010square fluctuations (RMSF) of residues of accurate CASP predictions. The correlation between the local resolution and pLDDT was less clear, especially when mobile domains were present. When the resolution allowed, assessment of features such as sidechains, using our variant of SMOC with local fragment alignment, indicated that even high\u2010quality predictions have room for improvement; on the other hand, some predictions fitted the density better in specific regions, indicating modeling discrepancies in the target. In one extreme case, a submitted target had regions of low\u2010resolution that limited unambiguous model building. In such cases, part of the target structure is essentially a prediction itself, with implications for the assessment. Experimental data remain essential for model\u2010free assessment of predictions and offer unique analyses such as comparisons to local resolution and thus flexibility.<\/jats:p>","DOI":"10.1002\/prot.70099","type":"journal-article","created":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:12:55Z","timestamp":1765483975000},"page":"447-459","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Cryo\u2010\n                    <scp>EM<\/scp>\n                    Analysis in\n                    <scp>CASP16<\/scp>"],"prefix":"10.1002","volume":"94","author":[{"given":"Thomas","family":"Mulvaney","sequence":"first","affiliation":[{"name":"Research Department of Integrative Virology Leibniz Institute of Virology (LIV)  Hamburg Germany"},{"name":"Center for Structural Systems Biology (CSSB), DESY  Hamburg Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5066-7178","authenticated-orcid":false,"given":"Andriy","family":"Kryshtafovych","sequence":"additional","affiliation":[{"name":"Genome Center University of California  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maya","family":"Topf","sequence":"additional","affiliation":[{"name":"Research Department of Integrative Virology Leibniz Institute of Virology (LIV)  Hamburg Germany"},{"name":"Center for Structural Systems Biology (CSSB), DESY  Hamburg Germany"},{"name":"Institute for Molecular Virology and Tumorvirology University Medical Center Hamburg\u2010Eppendorf (UKE)  Hamburg Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,12,11]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/80734"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.25817"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26216"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26644"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2007.11.016"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.108.139451"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010023\u201044593\u20101"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad721"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20104939\u20102763\u20100_17"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010020\u201001051\u2010w"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003819\u20102"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26223"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010025\u201009073\u20100"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26602"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798319016577"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4792"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt473"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj8754"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2016.03.007"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798325005923"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.70025"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adr2753"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.70043"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010025\u201058575\u2010y"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2221745120"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010024\u201008324\u2010w"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010022\u201014382\u20109"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.70040"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.3390\/cryst13111560"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad629"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798323001602"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798322010026"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798325001251"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1063\/4.0000860"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010024\u201002272\u2010z"},{"key":"e_1_2_10_37_1","doi-asserted-by":"crossref","unstructured":"B.Sava\u015f 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B.Barlas andE.Karaca \u201cExploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo\u2010EM Maps \u201d(2025) https:\/\/doi.org\/10.1101\/2025.07.25.666757.","DOI":"10.1101\/2025.07.25.666757"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2024.100724"}],"container-title":["Proteins: Structure, Function, and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.70099","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T07:42:44Z","timestamp":1767080564000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.70099"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,11]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1002\/prot.70099"],"URL":"https:\/\/doi.org\/10.1002\/prot.70099","archive":["Portico"],"relation":{},"ISSN":["0887-3585","1097-0134"],"issn-type":[{"value":"0887-3585","type":"print"},{"value":"1097-0134","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,11]]},"assertion":[{"value":"2025-10-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-03","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-11","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}