{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T15:53:07Z","timestamp":1778428387260,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012526","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T00:00:00Z","timestamp":1731628800000}}],"reference-count":33,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T00:00:00Z","timestamp":1730764800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006226","name":"Krell Institute","doi-asserted-by":"publisher","award":["DE-SC0020347"],"award-info":[{"award-number":["DE-SC0020347"]}],"id":[{"id":"10.13039\/100006226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014220","name":"Innovative Genomics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014220","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","award":["8802"],"award-info":[{"award-number":["8802"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["DP2AT011967"],"award-info":[{"award-number":["DP2AT011967"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant\n                    <jats:italic>Arabidopsis thaliana<\/jats:italic>\n                    and validated against a benchmark dataset of 172 manually-annotated LRR domains.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012526","type":"journal-article","created":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T13:35:16Z","timestamp":1730813716000},"page":"e1012526","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Structure-aware annotation of leucine-rich repeat domains"],"prefix":"10.1371","volume":"20","author":[{"given":"Boyan","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alois","family":"Cerbu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher J.","family":"Tralie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daven","family":"Lim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1679-0700","authenticated-orcid":true,"given":"Ksenia","family":"Krasileva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,11,5]]},"reference":[{"issue":"8","key":"pcbi.1012526.ref001","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The Arabidopsis information resource: making and mining the \u201cgold standard\u201d annotated reference plant genome","volume":"53","author":"TZ Berardini","year":"2015","journal-title":"Genesis"},{"issue":"1","key":"pcbi.1012526.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-018-1392-6","article-title":"Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions","volume":"19","author":"PC Bailey","year":"2018","journal-title":"Genome Biol"},{"issue":"7873","key":"pcbi.1012526.ref003","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"J Jumper","year":"2021","journal-title":"Nature"},{"issue":"suppl_2","key":"pcbi.1012526.ref004","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"RD Finn","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1012526.ref005","doi-asserted-by":"crossref","unstructured":"Tralie CJ, Berger M. 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