PDBePISA

PDBePISA analyzes macromolecular interfaces and predicts probable quaternary structures by applying chemical thermodynamics to Protein Data Bank (PDB) entries derived from X-ray diffraction experiments.

Key Features:

• Theoretical Framework: Applies chemical thermodynamics to evaluate affinity and entropy contributions that influence the size and symmetry of macromolecular complexes.
• Automatic Detection of Assemblies: Detects macromolecular assemblies within PDB entries derived from X-ray diffraction experiments with a reported success rate of 80–90%.
• Quaternary Structure Prediction: Predicts probable quaternary structures and assists in recovering biological units from experimental PDB data.
• Interface Analysis: Provides analysis of macromolecular interfaces and metrics relevant to protein–protein interactions and complex formation.

Scientific Applications:

• Macromolecular interface studies: Characterizes interfaces to support studies of protein–protein interactions and complex assembly.
• Quaternary structure assessment: Predicts and evaluates probable quaternary arrangements of macromolecular complexes.
• Thermodynamic interpretation: Interprets affinity and entropy contributions to understand drivers of complexation.
• Recovery of biological units: Identifies and annotates biological assemblies from X-ray crystallography entries in the PDB.

Methodology:

Applies chemical thermodynamics principles focusing on affinity and entropy to analyze macromolecular complexes and uses an automatic detection method on PDB entries from X-ray diffraction experiments to identify assemblies and predict quaternary structures.