{
  "abstract": "Structure integration with function, taxonomy and sequences (SIFTS) provides residue-level mappings between UniProt Knowledgebase sequences and Protein Data Bank structures and has historically been generated through internal Protein Data Bank in Europe (PDBe) pipelines. Here, PDBe-SIFTS is presented as a fully open-source, locally deployable implementation of this mapping framework. The pipeline combines fast, scalable sequence search using MMseqs2, an improved bounded scoring scheme for ranking candidate mappings, and residue-level mapping refinement based on backbone connectivity. PDBe-SIFTS is distributed as a Python package with command-line tools for (1) building a sequence search database, (2) identifying the best sequence-structure match, (3) one-to-one mapping at the residue level, and (4) generating SIFTS annotations in PDBx/mmCIF format. Benchmarking on the complete Protein Data Bank archive showed that MMseqs2 reduced archive-scale UniProtKB searches from hours with BLASTP to minutes, approximately 22-36 times faster, while curated mappings were recovered at top rank in 93.1% of cases. The remaining discrepancies mainly involved biologically ambiguous cases such as highly conserved proteins, chimeric constructs, or closely related orthologs. These results show that PDBe-SIFTS enables fast mapping, improving structural coherence in residue-level alignments while delivering the most up-to-date and accurate mappings, comparable to expert curation. Tool: https://github.com/PDBeurope/SIFTS. Quick start notebook with example: https://github.com/PDBeurope/SIFTS/tree/master/notebooks.",
  "abstract_shown": true,
  "affiliations": [
    "Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK.",
    "Protein Function Content, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK.",
    "Protein Function Development, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK."
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Adam Bellaiche",
      "orcid": "0000-0003-2465-2313"
    },
    {
      "affs": [
        0
      ],
      "name": "Preeti Choudhary",
      "orcid": "0000-0003-2340-3278"
    },
    {
      "affs": [
        0
      ],
      "name": "Sreenath Nair",
      "orcid": "0000-0002-6861-7627"
    },
    {
      "affs": [
        0
      ],
      "name": "Deborah Harrus",
      "orcid": "0000-0002-7651-672X"
    },
    {
      "affs": [
        1
      ],
      "name": "Conny Wing-Heng Yu",
      "orcid": "0000-0002-6478-5762"
    },
    {
      "affs": [
        0
      ],
      "name": "Syed Ahsan Tanweer",
      "orcid": "0000-0002-4793-3700"
    },
    {
      "affs": [
        0
      ],
      "name": "Genevieve Laura Evans",
      "orcid": "0000-0002-8612-9539"
    },
    {
      "affs": [
        1
      ],
      "name": "Stephanie W Lo",
      "orcid": "0000-0002-2182-0222"
    },
    {
      "affs": [
        2
      ],
      "name": "Maria J Martin",
      "orcid": "0000-0001-5454-2815"
    },
    {
      "affs": [
        0
      ],
      "name": "Jennifer R Fleming",
      "orcid": "0000-0003-4016-8740"
    },
    {
      "affs": [
        0
      ],
      "name": "Sameer Velankar",
      "orcid": "0000-0002-8439-5964"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e46xh5qhgnceb.bib",
  "cited_by": 0,
  "doi": "10.1002/pro.70819",
  "fulltext_url": "https://europepmc.org/articles/PMC13673133",
  "id": "e46xh5qhgnceb",
  "issns": [
    "0961-8368",
    "1469-896X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42885203",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2505|Enzyme Structure and Function"
    ]
  ],
  "openalex": "W7160264112",
  "pdf_url": "https://europepmc.org/articles/PMC13673133?pdf=render",
  "pmcid": "PMC13673133",
  "pmid": "42885203",
  "published": "2026-10-30",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/e46xh5qhgnceb.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42885203",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42885203"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:2505|Enzyme Structure and Function",
      "subfield": "materials-polymers"
    }
  ],
  "title": "PDBe-SIFTS: An open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.",
  "title_text": "PDBe-SIFTS: An open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:46Z",
  "url": "https://research.draconitic.com/paper/e46xh5qhgnceb",
  "venue": "Protein science : a publication of the Protein Society",
  "versions": []
}