Analyzing the simplicial decomposition of spatial protein structures

Area of Science:

• Structural biology
• Bioinformatics
• Computational chemistry

Background:

• The Protein Data Bank (PDB) houses over 45,000 protein and nucleic acid structures.
• X-ray crystallography is the primary method for data acquisition, involving extensive researcher effort.
• Data quality issues in the PDB hinder automated processing and analysis.

Purpose of the Study:

• To address data quality issues in the PDB.
• To create a cleaned and structured version of the PDB for enhanced analysis.
• To investigate geometric properties of atomic structures within biological macromolecules.

Main Methods:

• Rigorous restructuring of the entire PDB using graph-theoretical principles.
• Development of the Rich-Structure PDB (RS-PDB) database.
• Definition and analysis of simplicial complexes on heavy atoms and their tetrahedra.

Main Results:

• A cleaned and repaired database, RS-PDB, was successfully created.
• Simplicial complexes were defined on the heavy atoms of the PDB.
• Geometric properties of tetrahedra formed by atomic vertices were analyzed.

Conclusions:

• Distinct geometric differences were observed between simplices with varying atomic vertex types.
• Atomic neighborhoods, described by simplices, showed characteristic differences based on ligand atoms in proteins.