The DOI matches its Crossref record; 3 of the 4 references it cites were found in a registry or an index.
Announcing the worldwide Protein Data Bank
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“For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank3, Worldwide Protein Data Bank (wwPDB4), and UniProt5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD6) in the space sciences.”
From The FAIR Guiding Principles for scientific data management and stewardship (2016) · cites this paper as [4]
In the citing paper
“Structure quality was assessed using Molprobity56 before deposition in the PDB82,83”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [83]
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Citations
Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Self-citationThe protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
[30] Macromolecular crystallographic information file
Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J., & Fitzgerald, P. M. D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77032-0 · Cited by 170
Self-citation
Research works printed but not linked: 1
- Callaway, J. et al. Protein Data Bank Contents Guide: Atomic coordinate entry format description. (Brookhaven National Laboratory, 1996).
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50 years of PDB: A catalyst in structural biology
Bonvin, A. M. J. J. (2021) · Nature Methods · doi:10.1038/s41592-021-01138-y · Cited by 21
Thorn, A. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102368 · Cited by 16
Learning antibody sequence constraints from allelic inclusion
Jagota, M., Hsu, C., Mazumder, T., Sung, K., DeWitt, W. S., Listgarten, J., Matsen, F. A., Ye, C. J., & Song, Y. S. (2024) · doi:10.1101/2024.10.22.619760 · Cited by 2
“Initial experiments were run on ColabFold [49,50]; subsequent structure predictions were run with local installations of AlphaFold and ESMFold.”
Method
Metadata
- Authors
- Berman, H., Henrick, K., & Nakamura, H.
- Affiliations
- Institute for Protein Research, The University of Osaka (JP)
- Corresponding author
- Berman, Helen
- Venue
- Nature Structural & Molecular Biology
- Published
- 2003-12-01
- Volume
- 10
- Issue
- 12
- Pages
- 980-980
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W1995808589
- Cited by
- 3,093
- References
- 4
- Citations by year
- 2026: 155 · 2025: 212 · 2024: 266 · 2023: 274 · 2022: 238 · 2021: 240 · 2020: 208 · 2019: 217 · 2018: 141 · 2017: 138 · 2016: 125 · 2015: 89 · 2014: 93 · 2013: 105 · 2012: 103
- FWCI
- 11.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- Wellcome Trust
- European Molecular Biology Laboratory
- European Commission
- Japan Science and Technology Corporation
- Ministry of Education, Culture, Sports, Science and Technology
- National Institutes of Health
- Directorate for Biological Sciences
- Medical Research Council
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › 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
- wwPDB, structural biology, data repositories, data curation
- MeSH terms
- Archives, International Agencies, Computational Biology, Databases, Protein
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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.
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