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LoL-align maximizes a local log-odds score for proteins to be homologous, given their intra-protein\n                    <jats:italic>C<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>\u03b1<\/jats:italic>\n                    <\/jats:sub>\n                    \u2212\n                    <jats:italic>C<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>\u03b1<\/jats:italic>\n                    <\/jats:sub>\n                    distances. Here we show that LoL-align is markedly more sensitive in detecting remote homologs than TM-align and Dali on single- and multidomain benchmarks and achieves better alignment quality at 5\u201320 \u00d7 their speed. LoL-align is fully integrated into Foldseek.\n                  <\/jats:p>","DOI":"10.1038\/s41592-026-03249-w","type":"journal-article","created":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T21:56:24Z","timestamp":1792014984000},"page":"2147-2150","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["LoL-align: sensitive and fast probabilistic protein structure alignment"],"prefix":"10.1038","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2925-7585","authenticated-orcid":false,"given":"Lasse","family":"Reifenrath","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel","family":"van Kempen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gyuri","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soo Hyun","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1613-5537","authenticated-orcid":false,"given":"Mohammadreza","family":"Radnezhad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cameron L. 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The other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}