References and Examples
PDB entries are assigned a PDB ID that corresponds to a Digital Object Identifier (DOI) and in many cases, are described in a publication by the structure authors.
DOIs for PDB structures follow the format: 10.2210/pdbXXXX/pdb, where XXXX is replaced with the PDB ID (e.g., 10.2210/pdb4hhb/pdb). DOI citations should include the entry authors, deposition year, structure title, and DOI.
A PDB structure with a corresponding publication should be referenced by PDB ID and cited using both the corresponding DOI and publication.
PDB ID: 1ema
Ormo, M., Remington, S.J. (1996) Green fluorescent protein from Aequorea victoria doi: 10.2210/pdb1ema/pdb
Ormo, M., Cubitt, A.B., Kallio, K., Gross, L.A., Tsien, R.Y., Remington, S.J. (1996) Crystal structure of the Aequorea victoria green fluorescent protein Science 273: 1392-1395 doi: 10.1126/science.273.5280.1392
A PDB structure without a corresponding publication should be referenced by PDB ID and cited using the DOI Citation (entry authors, deposition year, structure title, and DOI):
PDB ID: 1ci0
Shi, W., Ostrov, D.A., Gerchman, S.E., Graziano, V., Kycia, H., Studier, B., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC) (1999) PNP Oxidase from Saccharomyces cerevisiae doi: 10.2210/pdb1ci0/pdb
RCSB PDB should be referenced with the URL rcsb.org and the following citation:
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne.
(2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
New website features and resources are also described in the 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: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
(2021) Nucleic Acids Research 49: D437–D451 doi: 10.1093/nar/gkaa1038
The RCSB PDB is a member of the worldwide PDB (wwPDB). The wwPDB should be cited with the URL www.wwpdb.org and the following citation:
H.M. Berman, K. Henrick, H. Nakamura (2003) Announcing the worldwide Protein Data Bank Nature Structural Biology 10 (12): 980.
Molecular images from Structure Summary pages and 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) (1981) Structure of a B-DNA dodecamer: conformation and dynamics 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.
Image of 1AOI (K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond (1997) Crystal structure of the core particle at 2.8Å resolution Nature 389: 251-260) created with NGL (A.S. Rose, A.R. Bradley, Y. Valasatava, J.D. Duarte, A. Prlić, P.W. Rose (2018) NGL viewer: web-based molecular graphics for large complexes. 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. Nucleic Acids Research. doi: 10.1093/nar/gkab314), and RCSB PDB.
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: 10.2210/rcsb_pdb/mom_YYYY_MM, where YYYY is the year, and MM the number of the month (one or two digits).
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 doi: 10.1002/bmb.21360
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 (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535-542.
The PDB archive was first announced in 1971: Protein Data Bank 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.
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