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References and Examples
A PDB structure entry should be cited with its PDB ID and 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 should be replaced with the desired PDB ID. The DOI can be used as part of a URL to obtain this data file (http://dx.doi.org/10.2210/pdb4hhb/pdb), or can be entered in a DOI resolver (such as http://www.crossref.org/) to automatically link to pdb4hhb.ent.gz on the main PDB ftp archive (ftp://ftp.wwpdb.org). For example, the DOI for PDB entry 4HHB is "10.2210/pdb4hhb/pdb". This links directly to the entry in the PDB file format on the FTP server.
- Images from this website should cite the RCSB PDB and
the 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).
The 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.
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): 98.
The RCSB PDB Molecule of the Month may be referenced using its Digital Object Identifier (DOI) and the author/s of the article. The DOIs for these features all have the same format: 10.2210/rcsb_pdb/mom_YYYY_MM, where YYYY should be replaced with the year, and MM with the number of the month (one or two digits). The DOI can be used as part of a URL to obtain this data file (http://dx.doi.org/10.2210/rcsb_pdb/mom_2003_5), or can be entered in a DOI resolver (such as http://www.crossref.org/).
For example, the DOI for the May 2003 feature on hemoglobin by Shuchismita Dutta and David S. Goodsell is "10.2210/rcsb_pdb/mom_2003_5".
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.