Dear all,
*By 2028*4-character PDB IDs (e.g.*1abc*) will be fully allocated. After
that, all new entries will be assigned*only extended PDB IDs*.
The new*extended PDB ID format
<https://www.wwpdb.org/documentation/pdb-id-extension-faq>will be 12
characters*, which includes a prefix pdb_ followed by 8 alphanumeric
characters, e.g.*pdb_1000axyz*. Thisnew ID format
<https://www.wwpdb.org/documentation/pdb-id-extension-faq>will enable
text mining detection of PDB entries in the published literature and
allow for more informative and transparent delivery of revised data
files.*/When submitting extended PDB IDs to journals and citing extended
PDB IDs in manuscripts, all 12 characters including prefix pdb_ should
be provided./*
APDB Beta Archive <https://www.wwpdb.org/ftp/pdb-beta-ftp-sites>is now
available to help community adopt extended PDB ID and PDBx/mmCIF format
during the transition phase. All files at this archive are re-organized
with extended PDB ID (including file naming and directories) at entry
level, mirroring the same data organization of thePDB Versioned Archive
<http://files-versioned.wwpdb.org/>.
All data files for a particular entry are stored in a single directory,
labeled based on a two-character hash generated from the penultimate two
characters of the PDB code, i.e.,
https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/<two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>.
The two-letter hash will be based on the second and third characters
from the last character. For example, PDB entry pdb_1abc5*67*8 will be
under*/67/*. This will maintain consistency with the current PDB
archive: PDB entry 1abc is under /ab.
File naming is standardized such that the file type is used for the
extension.
For example, file naming is changed
from*r116dsf.ent.gz*to*pdb_0000116d-sf.cif.gz*for the structure factor
file and from*pdb318d.ent.gz*to*pdb_0000318d.pdb.gz*for the legacy PDB
formatted coordinate file.
When four character PDB IDs are about to be consumed, this PDB Beta
Archive will replace the current PDB Archive (expect to be around
mid-2027) and entries with extended PDB IDs issued are not compatible
with PDB format. wwPDB encourages scientific journals, PDB community and
users to transition to PDBx/mmCIF format and adopt new PDB ID format as
earlier as possible.
For any further information please contact us [email protected].
Kind regards,
Deborah Harrus, on behalf of the wwPDB
--
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*I may send communications outside of your normal working hours. Please do not
feel obligated to reply until your normal working hours.*
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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