Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

Area of Science:

• Structural Biology
• Bioinformatics
• Molecular Biology

Background:

• Macromolecular complexes are vital for cellular functions.
• Atomic-level understanding of these complexes is crucial for biological research.
• The Protein Data Bank (PDB) stores structural data but lacks standardized assembly naming.

Purpose of the Study:

• To develop a method for standardizing the naming of macromolecular assemblies in the PDB.
• To improve the identification and contextualization of biological assemblies.
• To enhance the PDB's data quality and FAIR (Findable, Accessible, Interoperable, Reusable) attributes.

Main Methods:

• Leveraging external databases like Complex Portal, UniProt, and Gene Ontology.
• Developing a systematic approach to assign standard names and persistent identifiers to PDB assemblies.
• Applying the method to a large dataset of unique assemblies within the PDB.

Main Results:

• Successfully assigned standard names to over 90% of unique PDB assemblies.
• Provided persistent identifiers for each standardized assembly.
• Demonstrated significant improvement in data standardization and contextualization.

Conclusions:

• The developed method effectively standardizes macromolecular assembly data in the PDB.
• Enhanced data standardization improves the PDB's utility for research and education.
• Improved FAIR attributes of PDB data facilitate basic and translational research.