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References and Examples
PDB entries are assigned a PDB ID that corresponds to a Digital Object Identifier (DOI) and are frequently described in a publication by the structure authors.
DOIs for PDB structures follow the format: https://doi.org/10.2210/pdbXXXX/pdb, where XXXX is replaced with the PDB ID (e.g., https://doi.org/10.2210/pdb4hhb/pdb). DOI citations should include the entry authors, structure title, deposition year, and DOI.
A PDB structure with a corresponding publication should be referenced by PDB ID and cited using both the corresponding DOI citation and publication.
Example: PDB ID: 1ema
DOI Citation: M. Ormo, S.J. Remington, Green fluorescent protein from Aequorea victoria (1996) https://doi.org/10.2210/pdb1ema/pdb
Literature Citation: M. Ormo, A.B. Cubitt, K. Kallio, L.A. Gross, R.Y. Tsien, S.J. Remington, Crystal structure of the Aequorea victoria green fluorescent protein (1996) Science 273: 1392-1395 https://doi.org/10.1126/science.273.5280.1392
A PDB structure without a corresponding publication should be referenced by PDB ID and the DOI citation.
Example: PDB ID: 1ci0
DOI Citation: W. Shi, D.A. Ostrov, S.E. Gerchman, V. Graziano, H. Kycia, B. Studier, S.C. Almo, S.K. Burley, New York SGX Research Center for Structural Genomics (NYSGXRC), PNP Oxidase from Saccharomyces cerevisiae (1999) https://doi.org/10.2210/pdb1ci0/pdb
RCSB PDB should be referenced with the URL RCSB.org and the citation:
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne, The Protein Data Bank (2000) Nucleic Acids Research 28: 235-242 https://doi.org/10.1093/nar/28.1.235.
New website features and resources are also described in articles listed on our Publications page and in regular contributions to the Nucleic Acids Research Database Issue, including the most recent article:
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning (2023) Nucleic Acids Research 51: D488–D508 https://doi.org/10.1093/nar/gkac1077
The RCSB PDB is a member of the worldwide PDB (wwPDB). wwPDB should be cited with the URL wwpdb.org and the following citation:
H.M. Berman, K. Henrick, H. Nakamura Announcing the worldwide Protein Data Bank (2003) Nature Structural Biology 10:980 https://doi.org/10.1038/nsb1203-980.
Images from and/or of Structure Summary and Group Summary pages and tabs (including screenshots) should cite the RCSB PDB and PDB entry:
Image from the RCSB PDB (RCSB.org) of PDB ID 1BNA (H.R. Drew, R.M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R.E.Dickerson, Structure of a B-DNA dodecamer: conformation and dynamics (1981) Proc.Natl.Acad.Sci.USA 78: 2179-2183).
Images created using PDB data and other software should cite the PDB ID, the corresponding structure publication, and the molecular graphics program.
(K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond Crystal structure of the core particle at 2.8Å resolution (1997) Nature 389: 251-260) created with NGL (A.S. Rose, A.R. Bradley, Y. Valasatava, J.D. Duarte, A. Prlić, P.W. Rose NGL viewer: web-based molecular graphics for large complexes (2018) Bioinformatics 34: 3755–3758)
Images created using Mol* should cite the PDB ID, the corresponding structure publication, Mol* (D. Sehnal, S. Bittrich, M. Deshpande, R. Svobodová, K. Berka, V. Bazgier, S. Velankar, S.K. Burley, J. Koča, A.S. Rose (2021) Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures (2021) Nucleic Acids Research 49:W431-W437 https://doi.org/10.1093/nar/gkab314), and RCSB PDB.
Refer to AlphaFold Protein Structure Database for preferred citation of AlphaFold DB structures
Refer to ModelArchive for preferred citation of ModelArchive structures
Molecule of the Month illustrations are available under a CC-BY-4.0 license. Attribution should be given to David S. Goodsell and RCSB PDB. Molecule of the Month articles are copyrighted by RCSB PDB and the article authors. Text can be reprinted with permission, with attribution, and without the right to manipulate or change content. Contact firstname.lastname@example.org for permission.
Individual Molecule of the Month articles may be referenced using a Digital Object Identifier (DOI) with format: https://doi.org/10.2210/rcsb_pdb/mom_YYYY_MM, where YYYY is the year, and MM the number of the month (one or two digits, e.g. https://doi.org/10.2210/rcsb_pdb/mom_2020_1).
The reference for the Molecule of the Month series is:
The RCSB PDB "Molecule of the Month": Insights from 20 years of the Molecule of the Month (2020) BAMBed 48: 350-355 https://doi.org/10.1002/bmb.21360
Other usage of RCSB.org content (e.g., user guide documentation, statistics graphs, other screenshots) are available under a CC-BY-4.0 license. Attribution should be given to RCSB PDB as described above.
Brookhaven National Laboratory (BNL) PDB ceased operation on June 30, 1999. The original journal reference for the BNL PDB is: F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi, The Protein Data Bank: a computer-based archival file for macromolecular structures (1977) J. Mol. Biol. 112: 535-542.
The PDB archive was first announced in: Protein Data Bank (1971) Nature New Biology 233:223.
The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
All data provided by RCSB PDB programmatic APIs are available under the same license.
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