Dear all,
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 atfiles-nextgen.wwpdb.org
<https://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 atfiles.wwpdb.org <https://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
<https://www.wwpdb.org/news/news?year=2023>
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
athttps://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_00008aly/
* Both PDBx/mmCIF and PDBML are provided at this location. For entry
pdb_00008aly:
o pdb_00008aly_xyz-enrich.cif.gz
o pdb_00008aly_xyz-no-atom-enrich.xml.gz
Please [email protected] any questions.
Read this news on the wwPDB website:
https://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826
Kind regards,
Deborah Harrus
PDBe
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Deborah Harrus, Ph.D.
Lead Annotator
PDBe - 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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