Dear all,
Version 1.0 of the next generation archive repository (NextGen) for the
PDB archive was made available in early 2023
<http://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826>.
This “NextGen” archive hosts enriched atomic coordinate files, in both
PDBx/mmCIF and PDBML formats, with files available to download at
files-nextgen.wwpdb.org <https://files-nextgen.wwpdb.org/>.
The initial launch of the NextGen archive
<http://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826>
enriched coordinate files from the core PDB archive with sequence
annotation from external resources such as UniProt, SCOP2 and Pfam at
atom, residue, and chain levels. After consulting with user community,
this release has added intra-molecular connectivity for each residue
present in an entry, helping users transitioning from legacy PDB format
to PDBx/mmCIF format
<http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7>. The
connectivity information includes atom pairs, bond order, aromatic flag,
and stereochemistry as incorporated from the PDB Chemical Component
Dictionary (CCD). Users can extract this information from the
/_chem_comp_bond/ and /_chem_comp_atom/ categories of the
PDBx/mmCIF-formatted files from the NextGen archive.
To transition from legacy PDB format to PDBx/mmCIF, the file naming and
data are structured based on extended PDB IDs
<http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7> 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, e.g., PDB
entry 8aly:
https://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_00008aly/pdb_00008aly_xyz-enrich.cif.gz.
Users are encouraged to adopt PDBx/mmCIF format as early as possible.
Learn more about PDBx/mmCIF format and related software resources at
mmcif.wwpdb.org <https://mmcif.wwpdb.org/>.
In the future, the PDB NextGen archive will continue to be updated with
more enriched annotations from external database resources in the
metadata, building on the content already provided in the structure
model files in the PDB archive at files.wwpdb.org
<https://files.wwpdb.org/>.
Read this news online
<https://www.wwpdb.org/news/news?year=2023#649f0801d78e004e766a9680>
Kind regards,
Deborah Harrus
PDBe
--
-------------------------------------------------------------------
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
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
-------------------------------------------------------------------
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
