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New Biological Insights from Better Structure Models.

Wouter G Touw1, Robbie P Joosten2, Gert Vriend1

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Automated structure validation and refinement procedures significantly improve most X-ray protein structures in the Protein Data Bank (PDB). This process enhances data quality, leading to better biological insights.

Keywords:
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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Structure validation is crucial throughout the protein structure determination lifecycle.
  • Advancements in understanding protein structures, software, and computing power have enabled automated improvements.

Purpose of the Study:

  • To review structure validation and improvement processes.
  • To highlight resources for accessing improved Protein Data Bank (PDB) files and quality reports.
  • To demonstrate how post-deposition optimization yields better biological insights.

Main Methods:

  • Review of automated PDB_REDO procedures for structure refinement.
  • Analysis of structure validation resources and facilities.
  • Case studies illustrating the impact of optimized structures on biological interpretation.

Main Results:

  • Automated PDB_REDO can significantly improve approximately 85% of deposited X-ray structures.
  • Improved PDB files and quality reports are accessible through dedicated resources.
  • Optimized structures facilitate enhanced or novel biological discoveries.

Conclusions:

  • Automated structure validation and refinement are essential for high-quality structural data.
  • Post-deposition optimization of protein structures leads to improved scientific understanding and discovery.
  • Accessible resources provide valuable tools for researchers working with structural data.