{
  "abstract": "The ubiquitous availability of protein structures permits replacing sequence alignment with more accurate and sensitive structure alignment algorithms. LoL-align maximizes a local log-odds score for proteins to be homologous, given their intra-protein Cα − Cα 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 5–20 × their speed. LoL-align is fully integrated into Foldseek.",
  "abstract_shown": true,
  "affiliations": [
    "Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany",
    "School of Biological Sciences, Seoul National University, Seoul, South Korea",
    "Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea",
    "Korea Basic Science Institute, Ochang-center, Cheongju, South Korea",
    "Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, South Korea",
    "Biomedical Institute for Convergence at Sungkyunkwan University, Sungkyunkwan University, Suwon, South Korea",
    "Artificial Intelligence Institute, Seoul National University, Seoul, South Korea",
    "Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea",
    "Campus Institute Data Science (CIDAS), Göttingen, Germany"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Lasse Reifenrath",
      "orcid": "0009-0001-2925-7585"
    },
    {
      "affs": [
        0
      ],
      "name": "Michel van Kempen"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Gyuri Kim"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Soo Hyun Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "Mohammadreza Radnezhad",
      "orcid": "0009-0005-1613-5537"
    },
    {
      "affs": [
        1,
        3
      ],
      "name": "Cameron L. M. Gilchrist"
    },
    {
      "affs": [
        1,
        4,
        5
      ],
      "name": "Milot Mirdita",
      "orcid": "0000-0001-8637-6719"
    },
    {
      "affs": [
        1,
        6,
        7
      ],
      "name": "Martin Steinegger",
      "orcid": "0000-0001-8781-9753"
    },
    {
      "affs": [
        0,
        8
      ],
      "name": "Johannes Söding",
      "orcid": "0000-0001-9642-8244"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7xvh8ecrzx65t.bib",
  "cited_by": 1,
  "doi": "10.1038/s41592-026-03249-w",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13736684/",
  "id": "7xvh8ecrzx65t",
  "issns": [
    "1548-7091",
    "1548-7105"
  ],
  "landing_url": "https://doi.org/10.1038/s41592-026-03249-w",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Brief Communication"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7221754960",
  "pdf_url": "https://www.nature.com/articles/s41592-026-03249-w.pdf",
  "pmcid": "PMC13736684",
  "pmid": "42875594",
  "published": "2026-10-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7xvh8ecrzx65t.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T12:22:05Z",
      "native_id": "PMC13736684",
      "source": "pmc",
      "url": "https://doi.org/10.1038/s41592-026-03249-w"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "LoL-align: sensitive and fast probabilistic protein structure alignment",
  "title_text": "LoL-align: sensitive and fast probabilistic protein structure alignment",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T12:22:05Z",
  "url": "https://research.draconitic.com/paper/7xvh8ecrzx65t",
  "venue": "Nature Methods",
  "versions": []
}