Citing Structures in the PDB: IDs, citations, and DOIs
The contents of the PDB are in the public domain. Structures can be cited using their PDB ID and the published citation related to the structure.
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 DOI can then be used as part of a URL to obtain the entry's compressed data file in PDB format
or can be entered in a DOI resolver (such as http://www.crossref.org/) to automatically link to
pdb4hhb.ent.Z in 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 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
Detailed information for citing the use of data, structures (with examples), and images is available from the RCSB PDB home page under "General Information".
New Information and Statistics Available at BioSync
The BioSync website now contains updated beamline descriptions for operational US synchrotron beamlines as well as some basic information for almost all operational international beamlines.
PDB deposition statistics, grouped by site and beamline, can be found at biosync.rcsb.org. Galleries of structures, also grouped by site and beamline, are cross-linked to structure summary pages in the RCSB PDB. Tables of primary citations and some general information (phasing software, resolution, R-factors, etc.) are also provided. Most recently, similar tables and galleries have been added for structural genomics structures solved from synchrotron data.
BioSync (Structural Biology Synchrotron Users Organization) was formed in 1990 as a grassroots organization intended to promote access to synchrotron radiation. The BioSync resource, originally designed and hosted by UCSD/SDSC, has been updated and is now being maintained by the RCSB PDB.
Updates to beamline descriptions from local personnel as well as general comments and suggestions are most welcome at BioSync@rcsb.rutgers.edu.
Making Virus Models with Middle School Students
Annotators helped middle school students in New Jersey build 3D
models of virus structures as part of Princeton University's Science and Engineering Expo (March 22). For a copy of the template used to create paper virus models, please email email@example.com.
Annotators helped students create virus structures
Molecules of the Quarter
The Molecule of the Month series explores the function and
significance of selected biological macromolecules for a general
audience. The molecules featured this quarter were importins,
exosomes, and zinc fingers. The complete Molecule of the Month
features are accessible from www.pdb.org.