Dear ccp4bb,
The PDBe team is excited to unveil a new process for identifying protein
conformational states across the Protein Data Bank (PDB) archive. Using
deterministic clustering, we have developed a data pipeline that offers
unprecedented insights into the structural variability of proteins.
The pipeline considers all proteins in the PDB with 100% sequence
identity and calculates a global dissimilarity score called "GLOCON".
Chains with similar scores are clustered together. This process enables
us to explore the range of conformation across protein structures,
capturing both minor conformational differences and large domain movements.
The results of the data pipeline are available through PDBe-KB
aggregated views of proteins. Users can visualise the results per
UniProt accessions using the "3D view of superposed structures" button
to explore the structures in the Mol* viewer.
In a number of case studies, this clustering process can indicate
significant biological relevance. Some case studies, such as hexokinase,
aldose reductase and KaiB, demonstrate the ability of the pipeline to
identify distinct protein conformations and shed light on their
biological significance.
To find out more, view the full news item at
https://www.ebi.ac.uk/pdbe/news/illuminating-protein-conformational-landscapes-pdb-archive
We also encourage you to view our pre-print at
https://doi.org/10.1101/2023.07.13.545008
If you have any questions or would like further details, please feel
free to contact the team at pdbeh...@ebi.ac.uk.
Kind regards,
David
--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
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