[3dem] PDB NextGen Archive Now Provides Intra-molecular Connectivity
Justin Flatt
justin at rcsb.rutgers.edu
Thu Jul 6 09:34:19 PDT 2023
Version 1.0 of the next generation archive repository (NextGen) for the
PDB archive was made available in early 2023 [1]. 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
[2].
The initial launch of the NextGen archive [1] 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
[3]. 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 [3] 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://urldefense.com/v3/__https://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_00008aly/pdb_00008aly_xyz-enrich.cif.gz__;!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZKUiVl3-$ .
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 [4].
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 [5].
Links:
------
[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*63cedad9b5f08ee94ab73826__;Iw!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZJsNoU0z$
[2] https://urldefense.com/v3/__https://files-nextgen.wwpdb.org/__;!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZLyX_9XH$
[3] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*63ff72ccc031758bf1c30ff7__;Iw!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZE_t3rF1$
[4] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZIliVAVr$
[5] https://urldefense.com/v3/__https://files.wwpdb.org/__;!!Mih3wA!CRFTVzJnFgjXOpv4mPz9skZ153lwR3kklvT0BI8lkyMkwsCjPzcp6qR_7nuGCqzvYpLyM8xTRlqEJSECZOIj5EXG$
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