[wwPDB] Prototype of PDB NextGen Archive now available

A prototype of a next generation archive repository for the PDB is now available. The archive, called “NextGen”, hosts structural model files in PDBx/mmCIF and PDBML formats at files-nextgen.wwpdb.org. This enriched PDB archive provides annotation from external database resources in the metadata in addition to the content provided in the structure model files in the PDB main archive at files.wwpdb.org.

This prototype provides sequence annotation from external resources such as UniProt, SCOP2 and Pfam at atom, residue, and chain levels. This mapping information is derived from the Structure Integration with Function, Taxonomy and Sequence (SIFTS) project (https://www.ebi.ac.uk/pdbe/docs/sifts/), a service developed and maintained by the PDBe and UniProt teams at EMBL-EBI. Sequence mappings are provided in _pdbx_sifts_unp_segments and _pdbx_sifts_xref_db_segments categories for each segment, _pdbx_sifts_xref_db at residue level, and _atom_site at atom level.

The PDB NextGen Repository is currently updated monthly on the first Wednesday of the month at 00:00 UTC and is subject to change in the future. You can access these NextGen files at the following locations:

• wwPDB: https://files-nextgen.wwpdb.org, rsync://rsync-nextgen.wwpdb.org
• RCSB PDB (USA): https://files-nextgen.rcsb.org, rsync://rsync-nextgen.rcsb.org
• PDBe (UK): https://ftp.ebi.ac.uk/pub/databases/pdb_nextgen/
• PDBj (Japan): https://ftp-nextgen.pdbj.org

Data are structured based on entry ID with a two letter hash code, ‘third from last character’ and ‘second from last character’. This hash code will remain consistent once PDB ID codes are extended beyond four characters with the pdb_ prefix.

Some examples are shown below:

• Access entry pdb_00008aly at https://files-nextgen.wwpdb.org/data/entries/divided/al/pdb_00008aly/
• Both PDBx/mmCIF and PDBML are provided at this location. For entry pdb_00008aly:
  • pdb_00008aly_xyz-enrich.cif.gz
  • pdb_00008aly_xyz-no-atom-enrich.xml.gz

Please contact info@wwpdb.org with any questions.

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