News
Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files
08/01 
Journals, PDB users, and software developers should review code and begin to prepare for the change in format of PDB IDs and inclusion of PDB DOIs in PDBx/mmCIF fileswwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of ID codes for PDB and Chemical Component Dictionary (CCD) ID entries in the future. These extended formats are not supported by the legacy PDB file format.
As announced previously, wwPDB has extended PDB ID length to eight characters prefixed by ‘PDB’, e.g., pdb_00001abc.
Each PDB ID is issued a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors.
To help depositors provide information to journals, OneDep now displays the PDB ID and DOI on the submission confirmation page.
The extended PDB IDs and corresponding PDB DOIs, along with existing four character PDB IDs, are now included in the PDBx/mmCIF formatted files. Initially, this will only be available for updated and newly-released PDB entries, with an archive-wide update at a later date.
The additional accessions will be provided in the _database_2 PDBx/mmCIF category.
For example, PDB entry 1ABC will have the extended PDB ID (pdb_00001abc) and the corresponding PDB DOI (10.2210/pdb1abc/pdb).
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb
WWPDB D_1xxxxxxxxx ? ?
Once all available four-character PDB IDs have been consumed, newly-deposited PDB entries will only be issued extended PDB ID codes. These entries will only be distributed in PDBx/mmCIF format.
wwPDB asks journals, users, and software developers to review code and remove related limitations.
