Improving Protein Structure Models with Re-refinement
Author Information
Author(s): Robbie P. Joosten, Thomas Womack, Gert Vriend, Gérard Bricogne
Primary Institution: Radboud University Nijmegen Medical Centre
Hypothesis
Can automated re-refinement of PDB entries improve the accuracy of protein structure models?
Conclusion
Re-refinement can significantly enhance the quality of protein structure models by correcting inaccuracies in the original data.
Supporting Evidence
- Automated re-refinement improved R free values for all five PDB entries analyzed.
- Manual optimization further enhanced the quality of the structure models.
- The study highlights the importance of accurate metadata for effective re-refinement.
Takeaway
This study shows that we can make better models of proteins by going back and fixing old data with new tools. It's like cleaning up a messy room to find things you didn't see before.
Methodology
The study combined automated re-refinement with structure validation and manual intervention to improve five selected PDB entries.
Potential Biases
Potential bias due to the selection of PDB entries that were already known to have issues.
Limitations
The study was limited to only five PDB entries, which may not represent all PDB entries.
Digital Object Identifier (DOI)
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