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Instructions to Journals

While publication of a related paper is not required for depositing a structure to the PDB archive, the release of structural data in the PDB at the time of publication is recommended.

The wwPDB asks that journals provide the publication date and citation information for structure articles to make the publication of a report and the release of the corresponding PDB structure as simultaneous as possible. Questions not addressed below should be sent to journal@wwpdb.org.

How to Notify the wwPDB that a Structure Should be Released

Data in the PDB is released weekly; we are unable to provide data out of cycle.

To eliminate any delays between the publication of a report in a journal and the release of the corresponding structure, we request that the paper title, author list, related PDB ID(s), DOI, and publication date be sent to deposit@wwpdb.org two weeks prior to publication. An electronic form is available for submitting this information at http://citation.wwpdb.org/.

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 in time for release, the entry may be scheduled for a later update.

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 related experimental data (structure factor amplitudes/intensities and/or NMR restraints and chemical shifts) must be deposited at a member site of the Worldwide Protein Data Bank.

The PDB ID assigned after deposition should be included in the manuscript. Authors must also submit the PDB Summary Validation Report (provided after annotation by the wwPDB) for review at the time of submission.

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 deposit@wwpdb.org.

Electron microscopy-derived density maps (all averaging methods, including sub-tomogram averaging) must be deposited in EM Data Bank (EMDB; emdatabank.org). For electron tomographic studies with no averaging, deposition of one or more representative tomograms in EMDB is strongly recommended. In cases where PDB models have been fitted into EMDB maps, the correspondences between them should be clearly stated.

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

Biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes that meet the following criteria are accepted:

  • For polypeptide structures
    1. all gene products
    2. all naturally-occurring peptides that are non-ribosomal in origin
    3. all peptidic repeat units of larger polymers (such as fibrous and amyloid polymers)
    4. Non-biological synthetic peptides with at least 24 residues within a polymer chain
  • Polynucleotide structures of four or more residues
  • Polysaccharide structures of four or more residues

Detailed information is available at http://www.wwpdb.org/policy.

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) from the date of deposition (when a PDB ID is issued).
  • A journal policy of "release upon publication" takes precedence over the 6-month or one-year hold PDB policy.

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.

When is the PDB Archive Updated?

The PDB archive is updated at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

What is the deadline for requesting release of entries?

PDB entries are processed by the members of the wwPDB (RCSB, PDBe and PDBj). They are either released when the corresponding paper is published (HPUB), released on a particular date (HOLD), or released immediately (REL).

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.

When the release of HPUB structures is requested, the PDB staff routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update.

To be included in the next update, any required author correspondence should be sent to the appropriate wwPDB member by noon Thursday (local time):

  • RCSB PDB, USA (deposit@deposit.rcsb.org)
  • PDBe, U.K. (pdbhelp@ebi.ac.uk)
  • PDBj, Japan (adit@adit.protein.osaka-u.ac.jp)

All entries due for release are transferred to the RCSB PDB for final packaging into the master PDB ftp archive. These files are then released at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

Requests received after these cutoff times will be processed during the next update cycle.

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.


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