PACSY

PACSY integrates structural data from the Protein Data Bank (PDB), NMR chemical shift data from the Biological Magnetic Resonance Data Bank (BMRB), and structural classifications from the Structural Classification of Proteins (SCOP) into a relational database to enable combined analysis of three-dimensional coordinates, NMR-derived chemical shifts, torsion angles, solvent-accessible surface areas, and hydrophobicity scales.

Key Features:

• Data Integration: Integrates datasets from PDB, BMRB, and SCOP into a unified relational schema.
• Comprehensive Data Types: Stores three-dimensional coordinates, NMR-derived chemical shifts, torsion angles, solvent-accessible surface areas, and hydrophobicity scales.
• Relational Database Structure: Implements six types of relational tables interconnected via key identification numbers to maintain data coherence.
• Advanced Search Capabilities: Supports complex queries via RDBMS servers such as MySQL and PostgreSQL.
• Software Components: Provides PACSY Maker for database creation and PACSY Analyzer for database analysis.

Scientific Applications:

• Structural analysis: Enables exploration and combined analysis of protein three-dimensional structures alongside NMR chemical shifts.
• Chemical shift analysis: Supports analysis of NMR-derived chemical shifts in the context of atomic coordinates and derived torsion angles.
• Structural classification and modeling: Facilitates investigation of SCOP-based structural classifications and use of derived data (torsion angles, solvent-accessible surface areas, hydrophobicity) for structural modeling.

Methodology:

PACSY uses an RDBMS framework implemented on servers such as MySQL or PostgreSQL, employing six types of relational tables interconnected via key identification numbers to integrate and query data from PDB, BMRB, and SCOP.