[3dem] Paper Published about the PDB Beta Archive

[Justin Flatt]

A new publication describes the PDB Beta Archive [2] which incorporates 
the new updates, with the goal of supporting PDB users as they 
transition to the extended PDB ID and PDBx/mmCIF format. On July 21, 
2027, the PDB Beta Archive will replace the current PDB Archive when 
12-character PDB IDs are issued exclusively. Users are strongly 
encouraged to adapt to these changes in PDB data layout and content as 
soon as possible.

This PDB Beta Archive contains PDB entries in PDBx/mmCIF and PDBML 
formats, with extended PDB IDs in the datablock name. It is organized on 
an entry-level basis (e.g. all associated experimental and validation 
files for a particular entry are contained within the same directory) 
with extended PDB IDs used in the file and directory naming.

The wwPDB weekly update process was modified to create the PDB Beta 
Archive alongside the current PDB Archive. Both PDB Beta and the current 
main archives are updated in parallel each week and made available every 
Wednesday at 00:00 UTC.

> Protein Data Bank (PDB) Archive: a new architecture (beta) for 
> scalable, PDBx/mmCIF-based data distribution
> Zukang Feng, Balakumaran Balasubramaniyan, Gert-Jan Bekker, Jose M. 
> Duarte, Vladimir Guranovic, Jeremy Henry, Sreenath S. Nair, Ezra 
> Peisach, Dennis W. Piehl, Aditya Pingale, James Smith, Brinda Vallat, 
> Reiko Yamashita, Arthur Zalevsky, Kyle Morris,Jeff Hoch, Genji Kurisu, 
> Sameer Velankar, Stephen K. Burley, and Jasmine Y. Young
> (2026) _Acta Cryst_ D82: 982-989 doi: 10.1107/S2059798326006194 [1]

TRANSITION RESOURCES

  	* PDB ID Extension FAQ [3]
  	* PDB Beta Archive Overview: includes beta archive access, scripts, 
shortlink URLs, and other resources [2]
  	* PDBx/mmCIF software resources [4]
  	* Understanding PDBx/mmCIF format [5]
  	* PDBx/mmCIF User Guide [6]
  	* PDBx/mmCIF Dictionary [7]
  	* PDB -> PDBx/mmCIF correspondences [8]
  	* An online PDBx/mmCIF Editor [9]



Links:
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[1] https://urldefense.com/v3/__http://doi.org/10.1107/S2059798326006194__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaME-M33N$ 
[2] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-beta-ftp-sites__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaAhOQHO8$ 
[3] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/pdb-id-extension-faq__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaNqgu8Xs$ 
[4] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/software-resources.html__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaMymAFOF$ 
[5] 
https://urldefense.com/v3/__https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner**Bs-guide-to-pdbx-mmcif__;4oCZ!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaHpxdLr8$ 
[6] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/user-guide/guide.html__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaOSCd5ja$ 
[7] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaBE7PxP5$ 
[8] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaIwnBAJD$ 
[9] https://urldefense.com/v3/__https://pdbj.org/cif-editor/__;!!Mih3wA!CSYcSBhpne7r2iFzFyTgz_oCi71jGtrkRQJVidmf31x6LMa_lItP34BF-cvG6udx-AgGRFf-SJfG9SWQaKZaqWcN$ 
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