Citing PDB-files

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SME
SME's picture
Citing PDB-files

Hi

I was wondering how I should cite a structure found in a PDB-file. Both how it should be cited in text and how to cite it in the reference list.

First some explanation. At our department at the university, it is customary to cite with the authors name, i.e.:
"... the protein works this way (Berg et al., 2002)"
The litterature can then be found in the reference list as:
"Berg, J. M., Tymoczko, J. L. & Stryer L. (2002) Biochemistry 5th edtion, W. H. Freeman and Company, New York"

So lets say I have found a 3D-structure of Lysozyme, 1GE2.
How should it be cited? Both in the text and in the reference list. According to the link, the primary citation is
"Takano, K., Yamagata, Y., Yutani, K. Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme Proteins, v.44, pp.233-243, 2001"

But is this enough? Should the PDB-file "1GE2" be included somehow? How about when the file has been revided?

Thanks in advanced,
Stefan
Aalborg University, Denmark

Guy Sovak
Guy Sovak's picture
Dear Stefan,

Dear Stefan,
Welcome on board Scientist Solutions,
I hope you would find the answers for your questions over here, and that you could help answer questions that are posted here.
Please fill in your data in "My Bench Space"

Now for your question,
I went into the link that you gave and found the way that they are asking to be cited. So it is taken from there web page.
Usualy data from the internet have got a way to be cited and it is given within the web page.
So please se what I attached from their site:

Citing the RCSB PDB and PDB Structures
The contents of PDB are in the public domain.
Online and printed resources are welcome to include PDB data and images from the RCSB PDB website, and may be sold, as long as the images and data are not for sale as commercial items themselves, and their corresponding citations are included.
It is expected that the authors of an entry as well as the RCSB PDB be properly cited whenever their work is referred to:
Structures used from the PDB should be cited with the PDB ID and the JRNL reference. For example, structure 102L should be referenced as:
PDB ID: 102L
D.W.Heinz, W.A.Baase, F.W.Dahlquist, B.W.Matthews
How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme.
Nature 361 pp. 561 (1993)

Structures without a published reference can be cited with the PDB ID, author names, and title:
PDB ID: 2I6E Tyagi, R., Kumaran, D., Burley, S.K., Swaminathan, S., (New York Structural GenomiX Research Consortium) Crystal structure of a hypothetical protein belonging to Pfam:DUF178 from Deinococcus radiodurans

Structures may also be referenced using their Document Object Identifier (DOI). The DOIs for PDB structures all have the same format - 10.2210/pdbXXXX/pdb - where XXXX should be replaced with the desired PDB ID. 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.
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.Z on the main PDB ftp archive (ftp://ftp.rcsb.org).
The journal reference for the Research Collaboratory for Structural Bioinformatics PDB is:
H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne
The Protein Data Bank
Nucleic Acids Research, 28 pp. 235-242 (2000)
The RCSB PDB is a member of the worldwide PDB (wwPDB). The journal reference for the wwPDB is:
H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980
The RCSB PDB should also be referenced with the WWW address:
http://www.pdb.org/.

The Brookhaven National Laboratory 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.
J. Mol. Biol. 112 pp. 535-542 (1977)

Molecule of the Month installations and illustrations used should reference the featured structure, as in #1 above, and also credit the author and illustrator, David S. Goodsell of The Scripps Research Institute.

Protein Workshop can be referenced with
J.L. Moreland, A.Gramada, O.V. Buzko, Qing Zhang and P.E. Bourne
The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications.
BMC Bioinformatics, 6:21 (2005)

SME
SME's picture
Wow. Thanks for the fast and

Wow. Thanks for the fast and detailed response. I am pretty sure, I can cite the PDB-files correctly now. And I'll head right on to fill in my data in "My Bench Space".

Guy Sovak
Guy Sovak's picture
It is always our pleasure to

It is always our pleasure to help our friends scientists all over the world.
I know that you have also your share of knowlage and that you can help others like we helped you
Best regards
Guy