LEVELNET

LEVELNET represents and analyzes protein-protein interaction (PPI) networks as multilayered graphs to support structural and comparative investigation of PPIs focused on protein chains with available 3D structures from the Protein Data Bank (PDB).

Key Features:

• Multilayered Graph Representation: Represents PPI networks as multilayered graphs to decompose complex interaction networks into subnetworks for direct comparison.
• Integration with Structural Data: Integrates 3D structures from the Protein Data Bank (PDB) to provide structural evidence supporting protein interactions.
• Comparative Analysis: Compares PPI networks derived from computational experiments and homology transfer to assess differences across data sources.
• Biological Process Investigation: Links structural evidence to PPIs associated with specific biological processes to aid functional interpretation.
• Co-localization Assessment: Assesses co-localization of interaction partners within cellular contexts to inform interaction plausibility.
• Benchmark Creation: Generates PPI benchmarks with desired properties to support development and validation of computational models and experimental approaches.

Scientific Applications:

• Structural Biology: Supports interpretation of PPIs using 3D structural evidence from the Protein Data Bank (PDB).
• Systems Biology: Enables decomposition and comparison of interaction subnetworks to study network-level organization and dynamics.
• Bioinformatics: Provides benchmarks and comparative datasets for development and validation of PPI prediction and analysis methods, including those based on homology transfer and computational experiments.

Methodology:

Represents PPI networks as multilayered graphs; selects protein chains with available 3D structures from the Protein Data Bank (PDB); integrates structural evidence; performs comparative analysis of networks from computational experiments and homology transfer; assesses co-localization; and generates PPI benchmarks.