Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data
Abstract 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 bio...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-04-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02101-6 |
| _version_ | 1797846125783285760 |
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| author | Preeti Choudhary Stephen Anyango John Berrisford James Tolchard Mihaly Varadi Sameer Velankar |
| author_facet | Preeti Choudhary Stephen Anyango John Berrisford James Tolchard Mihaly Varadi Sameer Velankar |
| author_sort | Preeti Choudhary |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-09T17:49:53Z |
| format | Article |
| id | doaj.art-f525fdcb809742669e918419cf913c02 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-09T17:49:53Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-f525fdcb809742669e918419cf913c022023-04-16T11:06:36ZengNature PortfolioScientific Data2052-44632023-04-0110111310.1038/s41597-023-02101-6Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB dataPreeti Choudhary0Stephen Anyango1John Berrisford2James Tolchard3Mihaly Varadi4Sameer Velankar5Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Abstract 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.https://doi.org/10.1038/s41597-023-02101-6 |
| spellingShingle | Preeti Choudhary Stephen Anyango John Berrisford James Tolchard Mihaly Varadi Sameer Velankar Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data Scientific Data |
| title | Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data |
| title_full | Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data |
| title_fullStr | Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data |
| title_full_unstemmed | Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data |
| title_short | Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data |
| title_sort | unified access to up to date residue level annotations from uniprotkb and other biological databases for pdb data |
| url | https://doi.org/10.1038/s41597-023-02101-6 |
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