Dear all,
In October 2023, the wwPDB will roll out updated Chemical Component
Dictionary (CCD) data files with standardized atom naming and additional
annotation of protein backbone and terminal atoms within peptide
residues. Entries containing those updated CCDs will also be updated
accordingly. This will improve the Findability and Interoperability of
the PDB data, as well as open up new opportunities to use the updated
peptide residue annotation.
As part of this remediation process, we will add new data items to the
CCD files for peptide-linking components to label atoms that form the
backbone, N- or C-terminal groups. Three new CCD data items will be
added to the CCD category _chem_comp_atom as pdbx_backbone_flag,
pdbx_n-terminal_flag and pdbx_c-terminal_flag, flagging the backbone,
N-terminal and C-terminal atoms, respectively.
Furthermore, we will be standardizing the atom nomenclature of peptide
backbone atoms in CCD files to follow a standard convention. This will
follow a set of rules, outlined in the documentation linked below,
ensuring that atom nomenclature for carboxyl groups, amino groups and
side chain linked carbons (C-alpha) follow a standard atom nomenclature.
This will allow clear identification of backbone atoms for peptide
residues across the whole archive.
Detailed information about this work is available from the wwPDB
website, including PDBx/mmCIF dictionary extension and example files
(GitHub <https://github.com/wwPDB/backbone-extension>; Peptide Residues
Chemical Component Dictionary Remediation Documentation
<http://www.wwpdb.org/documentation/peptides-remediation>).
<I>Updated peptide CCDs will have standardized atom names and backbone /
N- and C- terminal annotation.</I>/
/
/Updated peptide CCDs will have standardized atom names and backbone /
N- and C- terminal annotation./
We encourage developers of software packages for refinement or
visualization of PDB data to review this information.
Questions or feedback? Contact deposit-h...@mail.wwpdb.org.
The peptide residues chemical component dictionary remediation project
is part of the protein chemical modifications (PCMs) and post
translational modifications (PTMs) remediation project, a wwPDB
collaborative project carried out principally by PDBe at EMBL-EBI, and
is funded by BBSRC grant number BB/V018779/1.
Read this news online:
https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687
Kind regards,
Deborah Harrus
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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
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