References and Examples
A PDB structure with a published reference can be cited with its PDB ID and corresponding structure publication. For example:
PDB ID: 102L
D.W. Heinz, W.A. Baase, F.W. Dahlquist, B.W. Matthews (1993) How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme Nature 361:561.
A PDB structure without a published reference can be cited using the PDB ID, author names, year of release, title, and DOI:
PDB ID: 1CI0
W. Shi, D.A. Ostrov, S.E. Gerchman, V. Graziano, H. Kycia, B. Studier, S.C. Almo, S.K. Burley, New York Structural GenomiX Research Consortium (NYSGXRC) (1999) The Structure of PNP Oxidase from S. cerevisiae doi: 10.2210/pdb1ci0/pdb
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).
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:
Stephen K Burley, Helen M. Berman, et al.
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
(2019) Nucleic Acids Research 47: D464–D474. doi: 10.1093/nar/gky1004.
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, A.S. Rose, J. Kovca, S.K. Burley, S. Velankar (2018) Mol*: Towards a common library and tools for web molecular graphics MolVA/EuroVis Proceedings. doi:10.2312/molva.20181103), 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 email@example.com 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": Inspiring a Molecular View of Biology (2015) PLoS Biol 13(5): e1002140. doi: 10.1371/journal.pbio.1002140
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.
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data. By using the materials available in the PDB archive, the user agrees to abide by the conditions described in the wwPDB Privacy and Usage Policy.
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