Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data Article Swipe
Preeti Choudhary
,
Stephen Anyango
,
John M. Berrisford
,
James Tolchard
,
Mihály Váradi
,
Sameer Velankar
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s41597-023-02101-6
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s41597-023-02101-6
More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41597-023-02101-6
- https://www.nature.com/articles/s41597-023-02101-6.pdf
- OA Status
- gold
- Cited By
- 9
- References
- 81
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4365137095Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s41597-023-02101-6Digital Object Identifier
- Title
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Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB dataWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-04-12Full publication date if available
- Authors
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Preeti Choudhary, Stephen Anyango, John M. Berrisford, James Tolchard, Mihály Váradi, Sameer VelankarList of authors in order
- Landing page
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https://doi.org/10.1038/s41597-023-02101-6Publisher landing page
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https://www.nature.com/articles/s41597-023-02101-6.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.nature.com/articles/s41597-023-02101-6.pdfDirect OA link when available
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UniProt, Protein Data Bank (RCSB PDB), Metadata, Computer science, Database, Information retrieval, XML, Interoperability, World Wide Web, Biology, Gene, BiochemistryTop concepts (fields/topics) attached by OpenAlex
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9Total citation count in OpenAlex
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2025: 2, 2024: 4, 2023: 3Per-year citation counts (last 5 years)
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81Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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