[3dem] Updated Annotation and Standardization of Peptide Residues

[Justin Flatt]

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://urldefense.com/v3/__https://github.com/wwPDB/backbone-extension__;!!Mih3wA!EU5rSQYhjVhJLfNatUNThJoupacH2EGzZX7Eeh7u-5vn_vqdhapRs9fZgTEX6Gg3EvB4w2EoFZpUsAE8njFZrz4o$ >; Peptide Residues 
Chemical Component Dictionary Remediation Documentation 
<https://urldefense.com/v3/__http://www.wwpdb.org/documentation/peptides-remediation__;!!Mih3wA!EU5rSQYhjVhJLfNatUNThJoupacH2EGzZX7Eeh7u-5vn_vqdhapRs9fZgTEX6Gg3EvB4w2EoFZpUsAE8nn5drhBk$ >).

Please see the wwPDB news for an example at 
https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*64bff95ed78e004e766a9687__;Iw!!Mih3wA!EU5rSQYhjVhJLfNatUNThJoupacH2EGzZX7Eeh7u-5vn_vqdhapRs9fZgTEX6Gg3EvB4w2EoFZpUsAE8nneEIEpY$ .

We encourage developers of software packages for refinement or 
visualization of PDB data to review this information.

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 at EMBL-EBI, and 
is funded by BBSRC grant number BB/V018779/1.

<https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*top__;Iw!!Mih3wA!EU5rSQYhjVhJLfNatUNThJoupacH2EGzZX7Eeh7u-5vn_vqdhapRs9fZgTEX6Gg3EvB4w2EoFZpUsAE8nsqOeFSb$ >
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