PCN-Miner

PCN-Miner constructs and analyzes Protein Contact Networks (PCNs) from Protein Data Bank (PDB) structures to characterize structural modules, allosteric regulation, and protein–protein interactions such as SARS-CoV-2 Spike protein binding to human ACE2 receptors.

Key Features:

• Data Importation: Imports protein structures directly from the Protein Data Bank (PDB) for downstream network analysis.
• PCN Generation and Modeling: Generates corresponding Protein Contact Networks (PCNs) for imported structures to model contacts and network topology.
• Analysis and Visualization: Applies clustering, embedding, established algorithms, and network metrics to analyze and visualize PCNs for insights into structure–function relationships.
• Application Versatility: Enables analyses relevant to allosteric regulation, modular substructure discovery, and protein–protein interactions including SARS-CoV-2 Spike–ACE2 binding.

Scientific Applications:

• Allosteric regulation analysis: Identifies modular substructures and pathways implicated in allosteric regulation within proteins.
• Protein–protein interaction analysis: Characterizes interactions such as SARS-CoV-2 Spike protein binding to human ACE2 receptors.
• Protein dynamics and function inference: Uses network metrics and embeddings to probe protein dynamics and infer functional sites.
• Drug design and virology research: Supports investigation of targets and mechanisms relevant to drug design, therapeutic interventions, and virology.

Methodology:

Imports PDB structures, generates Protein Contact Networks (PCNs), and applies clustering, embedding, established algorithms, and network metrics for analysis and visualization.