Information for Journals

While publication of a related paper is not required for depositing a structure to the Protein Data Bank (PDB) archive, many journals require deposition in the PDB as a condition of publication.

Questions not addressed below should be sent to info@wwpdb.org.

What is the PDB/wwPDB?

The Protein Data Bank (PDB) archive is the single repository for macromolecular structural data.

The PDB is managed by members of the Worldwide Protein Data Bank (wwPDB) to ensure that the data are freely and publicly available to the global community.

The wwPDB sites support systems to deposit data, and public websites and FTP servers to access the data.

Preferred Instructions to the Author

We suggest that journals adopt the policy below for papers describing experimentally-determined, biological macromolecules. The deposition of coordinates and experimental data, and their immediate public release at the time of the article's publication, provides the scientific community with the materials needed to fully understand the results presented in the manuscript.

For papers describing structures of biological macromolecules, the atomic coordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/msd), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu). The PDB ID should be included in the manuscript. Authors must agree to release the atomic coordinates and experimental data when the associated article is published. Questions relating to depositions should be sent to info@wwpdb.org.

Structures can be cited in the article using the PDB ID: The atomic coordinates and experimental data (code 1abc) have been deposited in the Protein Data Bank (www.wwpdb.org/).

wwPDB Data Deposition Policies

PDB depositions are restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules.

In addition to coordinate data, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) are required for PDB deposition.

wwPDB Data Release Policies

The release status of structures is determined at the time of deposition by the author.
Structures on hold are not released until publication or a longer period of time (up to one year) as requested by the author.
The status HPUB ("Hold for Publication") is used to indicate that a structure will be released when the corresponding journal article is published.

Publication is considered to be when the article is distributed by the publisher, either in print or electronically.
Structures are released when the PDB can confirm that the article corresponds with the entry.

The maximum hold for any structure is one year (even for HPUB structures).

How to Check if a Structure Has Been Deposited or Released

The status of an entry in the PDB archive may be checked by using the PDB ID in a search at one of these wwPDB sites: RCSB PDB, PDBe, or PDBj.

How to Notify the wwPDB that a Structure Should be Released

Journals are encouraged to regularly inform the wwPDB of publications.

The PDB archive is updated by 4:00 EST each Wednesday.

For a structure to be released as part of that update, release requests containing the PDB ID and related publication information should be sent to deposit@wwpdb.org by 12:00 noon EST on Thursday.

Requests received after this cutoff time will be processed during the next update cycle.

Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release. If this is not accomplished within that release cycle, the entry may be scheduled for released in a later update.

When is the PDB Archive Updated?