The Protein Data Bank: unifying the archive
Open accessAbstract
The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.
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- Authors
- Westbrook, J.
- Affiliations
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Westbrook, J.
- ORCID
- Westbrook, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-01-01
- Volume
- 30
- Issue
- 1
- Pages
- 245-248
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC99110
- OpenAlex
- W2147809382
- Cited by
- 309
- References
- 13
- Citations by year
- 2026: 6 · 2025: 11 · 2024: 3 · 2023: 6 · 2022: 8 · 2021: 13 · 2020: 6 · 2019: 9 · 2018: 8 · 2017: 13 · 2016: 10 · 2015: 4 · 2014: 9 · 2013: 8 · 2012: 8
- FWCI
- 27.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- Universität zu Köln
- National Institutes of Health
- National Institute of General Medical Sciences
- U.S. National Library of Medicine
- Biological and Environmental Research
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- Protein Data Bank, biological macromolecules, mmCIF, data validation, data format conversion
- MeSH terms
- Amino Acid Sequence, Animals, Archives, Database Management Systems, Enzymes, Forecasting, Ligands, Terminology as Topic, Polymers, Protein Conformation, Proteins, Quality Control, Stereoisomerism, User-Computer Interface, Information Storage and Retrieval, Internet, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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