Protein Data Bank: the single global archive for 3D macromolecular structure data
Open accessAbstract
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
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Since the mid-1950s, the scientific community has determined over 180,000 structures of proteins, nucleic acids, and complexes in atomic detail and archived them in the PDB.
“Since the mid-1950s, the scientific community has been using ever-more advanced experimental methods to determine over 180 000 structures of proteins, nucleic acids, and complexes in atomic detail, and archive them in the PDB, the single worldwide archive of experimental macromolecular structure data managed by the wwPDB consortium (21).”
From AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models (2022) · cites this paper as [21]
The final structures were validated using the wwPDB validation tool and the Protein Structure Validation Suite (PSVS).
“The final structures were validated using the wwPDB validation tool79,80 (https://validate-rcsb-east.wwpdb.org/validservice/) and the Protein Structure Validation Suite (PSVS)81.”
From Predicting multiple conformations via sequence clustering and AlphaFold2 (2024) · cites this paper as [80]
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Self-citationThe FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423 · see citing works
Announcing the worldwide Protein Data Bank
Berman, H., Henrick, K., & Nakamura, H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1203-980 · Cited by 3,093 · see citing works
Self-citationUlrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y., Lin, J. C., Livny, M., Mading, S., Maziuk, D., Miller, Z., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm957 · Cited by 1,472 · see citing works
Self-citationThe Cambridge Structural Database in Retrospect and Prospect
Groom, C. R., & Allen, F. H. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201306438 · Cited by 1,129 · see citing works
Collaboration gets the most out of software
Morin, A., Eisenbraun, B., Key, J., Sanschagrin, P. C., Timony, M. A., Ottaviano, M., & Piotr Sliz, A. (2013) · eLife · doi:10.7554/elife.01456 · Cited by 1,095 · see citing works
Abola, E. E., Bernstein, F. C., & Koetzle, T. F. (1984) · Springer eBooks · doi:10.1007/978-1-4899-0375-4_26 · Cited by 739 · see citing works
Outcome of the first electron microscopy validation task force meeting
Henderson, R., Sali, A., Baker, M. L., Carragher, B., Devkota, B., Downing, K. H., Egelman, E. H., Feng, Z., Frank, J., Grigorieff, N., et al. (2012) · Structure · doi:10.1016/j.str.2011.12.014 · Cited by 505 · see citing works
Self-citationA New Generation of Crystallographic Validation Tools for the Protein Data Bank
Read, R. J., Adams, P. D., Arendall, W. B., Brünger, A. T., Emsley, P., Joosten, R. P., Kleywegt, G. J., Krissinel, E., Lütteke, T., Otwinowski, Z., et al. (2011) · Structure · doi:10.1016/j.str.2011.08.006 · Cited by 468 · see citing works
Self-citationEMPIAR: a public archive for raw electron microscopy image data
Iudin, A., Korir, P. K., Torres, J. S., Kleywegt, G. J., & Patwardhan, A. (2016) · Nature Methods · doi:10.1038/nmeth.3806 · Cited by 318 · see citing works
Self-citationSASBDB, a repository for biological small-angle scattering data
Valentini, E., Kikhney, A., Previtali, G., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1047 · Cited by 307 · see citing works
Validation of Structures in the Protein Data Bank
Gore, S., Sanz-García, E., Hendrickx, P., Gutmanas, A., Westbrook, J., Yang, H.-W., Feng, Z.-K., Baskaran, K., Berrisford, J., Hudson, B., et al. (2017) · Structure · doi:10.1016/j.str.2017.10.009 · Cited by 245 · see citing works
Self-citationCrystallography: Protein Data Bank
(1971) · Nature New Biology · doi:10.1038/newbio233223b0 · Cited by 221 · see citing works
Gaieb, Z., Liu, S., Gathiaka, S., Chiu, M., Yang, H., Shao, C., Feher, V. A., Walters, W. P., Kuhn, B., Rudolph, M. G., et al. (2018) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-017-0088-4 · Cited by 193 · see citing works
Self-citationWestbrook, J., Shao, C., Feng, Z.-K., Zhuravleva, M., Velankar, S., & Young, J. Y. (2015) · Bioinform. · doi:10.1093/bioinformatics/btu789 · Cited by 177 · see citing works
Self-citationOutcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Šali, A., Berman, H. M., Schwede, T. F., Trewhella, J., Kleywegt, G. J., Burley, S. K., Markley, J. L., Nakamura, H., Adams, P. D., Bonvin, A. M. J. J., et al. (2015) · Structure · doi:10.1016/j.str.2015.05.013 · Cited by 170 · see citing works
Self-citationHaas, J., Barbato, A., Behringer, D., Studer, G., Roth, S., Bertoni, M., Mostaguir, K., Gumienny, R., & Schwede, T. (2018) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25431 · Cited by 168 · see citing works
Recommendations of the wwPDB NMR Validation Task Force
Montelione, G. T., Nilges, M., Bax, A., Güntert, P., Herrmann, T., Richardson, J. S., Schwieters, C. D., Vranken, W., Vuister, G. W., Wishart, D. S., et al. (2013) · Structure · doi:10.1016/j.str.2013.07.021 · Cited by 162 · see citing works
Self-citationYoung, J. Y., Westbrook, J., Feng, Z., Sala, R., Peisach, E., Oldfield, T. J., Sen, S., Gutmanas, A., Armstrong, D. R., Berrisford, J. M., et al. (2017) · Structure · doi:10.1016/j.str.2017.01.004 · Cited by 159 · see citing works
Self-citationPDBML: the representation of archival macromolecular structure data in XML
Westbrook, J., Ito, N., Nakamura, H., Henrick, K., & Berman, H. M. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti082 · Cited by 150 · see citing works
Self-citationKinjo, A. R., Bekker, G., Suzuki, H., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw962 · Cited by 148 · see citing works
Self-citationKinjo, A. R., Suzuki, H., Yamashita, R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr811 · Cited by 139 · see citing works
Self-citationNew electron microscopy database and deposition system
Tagari, M., Newman, R., Chagoyen, M., et al. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02176-x · Cited by 139 · see citing works
Remediation of the protein data bank archive
Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm937 · Cited by 139 · see citing works
Self-citationA public database of macromolecular diffraction experiments
Grabowski, M., Langner, K. M., Cymborowski, M., Porebski, P. J., Sroka, P., Zheng, H., Cooper, D. R., Zimmerman, M. D., Elsliger, M., Burley, S. K., et al. (2016) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798316014716 · Cited by 111 · see citing works
Self-citationPDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models
Burley, S. K., Kurisu, G., Markley, J. L., et al. (2017) · Structure · doi:10.1016/j.str.2017.08.001 · Cited by 106 · see citing works
Self-citationImplementing an X-ray validation pipeline for the Protein Data Bank
Gore, S. P., Velankar, S. S., & Kleywegt, G. J. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911050359 · Cited by 104 · see citing works
Self-citationThe challenge of modeling protein assemblies: the CASP12‐CAPRI experiment
Lensink, M. F., Velankar, S. S., Baek, M., Heo, L., Seok, C., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25419 · Cited by 95 · see citing works
Self-citationVallat, B. K., Webb, B., Westbrook, J., Šali, A., & Berman, H. M. (2018) · Structure · doi:10.1016/j.str.2018.03.011 · Cited by 93 · see citing works
Self-citationDoreleijers, J. F., Mading, S., Maziuk, D., et al. (2003) · Journal of Biomolecular NMR · doi:10.1023/a:1023514106644 · Cited by 89 · see citing works
Self-citationPDBe: towards reusable data delivery infrastructure at protein data bank in Europe
Mir, S., Alhroub, Y., Anyango, S., Armstrong, D. R., Berrisford, J. M., Clark, A. R., Conroy, M. J., Dana, J. M., Deshpande, M., Gupta, D. S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1070 · Cited by 83 · see citing works
Self-citationTrewhella, J., Hendrickson, W. A., Kleywegt, G. J., Šali, A., Sato, M., Schwede, T. F., Svergun, D. I., Tainer, J. A., Westbrook, J., & Berman, H. M. (2013) · Structure · doi:10.1016/j.str.2013.04.020 · Cited by 82 · see citing works
Self-citationValidation of ligands in macromolecular structures determined by X-ray crystallography
Smart, O. S., Horský, V., Gore, S. P., Vařeková, R. S., Bendová, V., Kleywegt, G. J., & Velankar, S. S. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318002541 · Cited by 80 · see citing works
Self-citationSTAR/mmCIF: An ontology for macromolecular structure
Westbrook, J., & Bourne, P. E. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.2.159 · Cited by 77 · see citing works
Self-citationOutcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
Adams, P. D., Aertgeerts, K., Bauer, C. B., Bell, J. A., Berman, H. M., Bhat, T. N., Blaney, J., Bolton, E., Bricogne, G., Brown, D. G., et al. (2016) · Structure · doi:10.1016/j.str.2016.02.017 · Cited by 67 · see citing works
Self-citationYoung, J. Y., Westbrook, J., Feng, Z., Peisach, E., Persikova, I., Sala, R., Sen, S., Berrisford, J. M., Swaminathan, G. J., Oldfield, T. J., et al. (2018) · Database · doi:10.1093/database/bay002 · Cited by 59 · see citing works
Self-citationEvaluation of the template-based modeling in CASP12
Kryshtafovych, A., Monastyrskyy, B., Fidelis, K., Moult, J., Schwede, T., & Tramontano, A. (2017) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25425 · Cited by 55 · see citing works
NMR Exchange Format: a unified and open standard for representation of NMR restraint data
Gutmanas, A., Adams, P. D., Bardiaux, B., et al. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3041 · Cited by 53 · see citing works
Self-citationAbbott, S., Iudin, A., Korir, P. K., et al. (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.48 · Cited by 21 · see citing works
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
Young, J. Y., Feng, Z., Dimitropoulos, D., et al. (2013) · Database · doi:10.1093/database/bat079 · Cited by 16 · see citing works
Self-citationSTAR/CIF macromolecular NMR data dictionaries and data file formats
Ulrich, E. L., Argentar, D., Klimowicz, A., et al. (1996) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767396076519 · Cited by 10 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 1
- [1]Protein Data Bank Protein Data Bank. Nat. New Biol. 1971; 233: 223.20480989
Cited by
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · see citing works
Self-citationProtein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · see citing works
Self-citationFast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2022) · doi:10.1101/2022.02.07.479398 · Cited by 2,598 · see citing works
Fast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01773-0 · Cited by 2,596 · see citing works
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1038 · Cited by 1,581 · see citing works
Self-citationUsing machine learning approaches for multi-omics data analysis: A review
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A structural biology community assessment of AlphaFold2 applications
Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675 · see citing works
Self-citationPredicting multiple conformations via sequence clustering and AlphaFold2
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- Authors
- wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., Liang, Y., Lowe, R., Peisach, E., Periskova, I., Randle, C., Rose, A., Sekharan, M., Shao, C., Tao, Y.-P., Valasatava, Y., Voigt, M., Westbrook, J., Young, J., Zardecki, C., Zhuravleva, M., Kurisu, G., Nakamura, H., Kengaku, Y., Cho, H., Sato, J., Kim, J. Y., Ikegawa, Y., Nakagawa, A., Yamashita, R., Kudou, T., Bekker, G.-J., Suzuki, H., Iwata, T., Yokochi, M., Kobayashi, N., Fujiwara, T., Velankar, S., Kleywegt, G. J., Anyango, S., Armstrong, D. R., Berrisford, J. M., Conroy, M. J., Dana, J. M., Deshpande, M., Gane, P., Gáborová, R., Gupta, D., Gutmanas, A., Koča, J., Mak, L., Mir, S., Mukhopadhyay, A., Nadzirin, N., Nair, S., Patwardhan, A., Paysan-Lafosse, T., Pravda, L., Salih, O., Sehnal, D., Varadi, M., Vařeková, R., Markley, J. L., Hoch, J. C., Romero, P. R., Baskaran, K., Maziuk, D., Ulrich, E. L., Wedell, J. R., Yao, H., Livny, M., & Ioannidis, Y. E.
- Affiliations
- European Bioinformatics Institute (GB)
- University of Wisconsin–Madison (US)
- Central European Institute of Technology (CZ)
- UConn Health (US)
- Athena Research and Innovation Center In Information Communication & Knowledge Technologies (GR)
- ORCID
- Burley, Stephen K
- Berman, Helen M
- Bhikadiya, Charmi
- Chen, Li
- Costanzo, Luigi Di
- Dutta, Shuchismita
- Feng, Zukang
- Ghosh, Sutapa
- Goodsell, David S
- Guzenko, Dmytro
- Hudson, Brian P
- Peisach, Ezra
- Rose, Alexander
- Sekharan, Monica
- Shao, Chenghua
- Voigt, Maria
- Westbrook, John
- Young, Jasmine
- Zardecki, Christine
- Kurisu, Genji
- Nakamura, Haruki
- Nakagawa, Atsushi
- Bekker, Gert-Jan
- Suzuki, Hirofumi
- Iwata, Takeshi
- Yokochi, Masashi
- Kobayashi, Naohiro
- Fujiwara, Toshimichi
- Velankar, Sameer
- Kleywegt, Gerard J
- Anyango, Stephen
- Armstrong, David R
- Berrisford, John M
- Conroy, Matthew J
- Dana, Jose M
- Deshpande, Mandar
- Gane, Paul
- Gáborová, Romana
- Gupta, Deepti
- Gutmanas, Aleksandras
- Koča, Jaroslav
- Mak, Lora
- Mir, Saqib
- Mukhopadhyay, Abhik
- Nadzirin, Nurul
- Nair, Sreenath
- Patwardhan, Ardan
- Salih, Osman
- Sehnal, David
- Vařeková, Radka
- Markley, John L
- Hoch, Jeffrey C
- Romero, Pedro R
- Baskaran, Kumaran
- Wedell, Jonathan R
- Livny, Miron
- Ioannidis, Yannis E
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-24
- Volume
- 47
- Issue
- D1
- Pages
- D520-D528
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6324056
- OpenAlex
- W2898210859
- Cited by
- 1,163
- References
- 41
- Citations by year
- 2026: 140 · 2025: 183 · 2024: 193 · 2023: 186 · 2022: 151 · 2021: 149 · 2020: 100 · 2019: 54 · 2018: 5 · 2013: 1
- FWCI
- 28.84
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Department of Energy (NSF-DBI 1338415)
- Wellcome Trust (88944, 104948)
- Biotechnology and Biological Sciences Research Council (BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1)
- European Union (284209, 675858)
- National Institutes of Health (R01GM109046)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- Protein Data Bank, wwPDB, atomic coordinates, structural validation, biocuration, protein structure, protein-ligand complex
- MeSH terms
- DNA, Metals, Models, Molecular, Molecular Conformation, Nucleic Acid Conformation, Protein Conformation, RNA, 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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