PISA

PISA (Protein Interfaces, Surfaces and Assemblies) analyzes PDB entries from X-ray crystallography to identify macromolecular assemblies and compute thermodynamic properties, including affinity and entropy, to infer biologically relevant complexes.

Key Features:

• Detection of macromolecular assemblies: Automatically detects macromolecular assemblies within PDB entries derived from X-ray diffraction using a method rooted in chemical thermodynamics.
• Calculation of affinity and entropy: Implements theoretical approaches to calculate affinity and the entropic contribution to complexation, explicitly considering entropy's influence on complex size and symmetry.
• Performance on biological unit recovery: Recovers biological units from X-ray crystallography data with a reported success rate of 80–90%.

Scientific Applications:

• Structural characterization: Provides insights into the assembly and interaction of proteins for structural biology studies.
• Protein–protein interaction analysis: Aids analysis of protein–protein interfaces and macromolecular complexes.
• Functional and therapeutic studies: Supports studies of enzymatic function and the development of therapeutics targeting specific protein complexes.

Methodology:

The method applies chemical thermodynamics to analyze PDB entries from X-ray diffraction, automatically detecting assemblies and computing affinity and entropy using theoretical approaches.