[3dem] Backbone Annotation and Standardization of Peptide Residues is Now Live

[Justin Flatt]

The wwPDB has rolled 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 have been updated accordingly. This 
improves the Findability and Interoperability of the PDB data and opens 
up new opportunities to use the updated peptide residue annotation.

As announced previously [1], new data items have been added 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 have been 
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 have standardized the atom nomenclature of peptide 
backbone atoms in CCD files to follow a standard convention. This 
follows a set of rules, outlined in our documentation [2], ensuring that 
atom nomenclature for carboxyl groups, amino groups and side chain 
linked carbons (C-alpha) follow a standard atom nomenclature. This 
allows clear identification of backbone atoms for peptide residues 
across the whole archive.

_Updated peptide CCDs will have standardized atom names and backbone / 
N- and C- terminal annotation._

Questions or feedback? Contact deposit-help at 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 [3] at EMBL-EBI 
[4], and is funded by BBSRC grant number BB/V018779/1.

Links:
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[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*64bff95ed78e004e766a9687__;Iw!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsp6SCKQ_$ 
[2] https://urldefense.com/v3/__http://www.wwpdb.org/documentation/peptides-remediation__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsqWVksk0$ 
[3] https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzsuyXIfgW$ 
[4] https://urldefense.com/v3/__https://www.ebi.ac.uk/__;!!Mih3wA!G3dpeB_s6LT7s6UWaZUFfaf5FjeNdsSZlftYSWzLpJt0IrXYqLpykyscb3sSsPGiVpb0En8GKBmvQnNzstf00Py2$ 
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