ProDGe

ProDGe predicts and visualizes domain–domain interactions to map and infer protein–protein interactions at the domain level for comparative and evolutionary analysis.

Key Features:

• Visualization and Prediction: Visualizes known domain–domain interactions and predicts novel domain-mediated protein–protein interactions at the domain level.
• Comprehensive Dataset Integration: Integrates protein, domain, and interaction data from UniProt, Pfam, DOMINE, and IntAct.
• Confidence Classification: Assigns novel domain–domain interactions to four confidence classes based on domain interaction reliability.
• Cross-Species Homology Identification: Identifies homologous interaction partners across species using sequence similarity.
• Empirical Validation and Comparison: Compares experimentally identified interactions from IntAct with domain interactions from DOMINE across six species, reporting that 31.13% of IntAct interactions map to domain-level interactions.

Scientific Applications:

• Protein interaction network analysis: Maps and refines protein–protein interaction networks at the domain level to elucidate interaction interfaces and connectivity.
• Experimental hypothesis generation and data interpretation: Generates hypotheses for experimental validation and aids interpretation of interaction data by predicting novel domain-mediated interactions and homologous partners.
• Evolutionary conservation and target identification: Analyzes evolutionary conservation of interactions to inform molecular mechanism studies and identify candidate therapeutic targets in understudied organisms.

Methodology:

Uses UniProt, Pfam, DOMINE, and IntAct data; identifies homologous partners via sequence similarity; classifies predicted domain interactions into four confidence classes based on domain interaction reliability; and compares DOMINE domain interactions to experimentally identified IntAct interactions across six species (31.13% mapping).