References and Examples
Cite a PDB structure entry using its PDB ID and corresponding primary reference. 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.
An entry without a published reference can be cited with the PDB ID, author names, and title:
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). The Structure of PNP Oxidase from S. cerevisiae
An entry may also be referenced using its Digital Object Identifier (DOI). The DOIs for PDB entries all have the same format: 10.2210/pdbXXXX/pdb, where XXXX is replaced with the PDB ID (e.g., 10.2210/pdb4hhb/pdb)
The DOI can be used as part of a URL (http://dx.doi.org/10.2210/pdb4hhb/pdb), or can be entered in a DOI resolver (http://www.crossref.org/) to automatically link to the entry on the PDB FTP archive (ftp://ftp.wwpdb.org).
RCSB PDB should be referenced with the URL www.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:
Peter W. Rose, Andreas Prlić, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S. Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huangwang Yang, Jasmine Y. Young, Christine Zardecki, Helen M. Berman, Stephen K. Burley.
(2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information Nucleic Acids Research, 45: D271-D281.
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 (www.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 and the molecular graphics program used.
Image of 1AOI (K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond (1997) structure of the core particle at 2.8 A resolution Nature 389: 251-260) created with Protein Workshop (J.L. Moreland, A. Gramada, O.V. Buzko, Q. Zhang, P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics 6:21).
Images created using the NGL Viewer should include the PDB ID and associated publication, the NGL Viewer (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 (doi:10.1093/bioinformatics/bty419), 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": 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.
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