PINALOG

PINALOG aligns protein–protein interaction (PPI) networks by integrating protein sequences, functional annotations, and network topology to identify conserved subnetworks and predict protein functions and complexes across species.

Key Features:

• Data integration: Integrates protein sequences, functional annotations, and topological (network) data to perform PPI network alignments.
• Cross-species network alignment: Aligns PPI networks between species such as human and yeast to identify conserved subnetworks, including those related to proteasome activity and transcription regulation.
• Conserved subnetwork detection: Identifies equivalent regions in networks that represent conserved pathways and interactions across organisms.
• Function prediction in low-similarity regions: Predicts protein functions in regions of low sequence similarity where sequence-based methods such as PSI-BLAST may fail.
• Protein complex prediction: Predicts protein complexes to reveal structural and functional organization within cells.

Scientific Applications:

• Comparative interactomics: Compare interactomes to study species evolution and conserved molecular machinery.
• Conserved component identification: Identify conserved functional components across organisms for functional annotation transfer.
• Protein function annotation: Predict functions for proteins with ambiguous or low-sequence-similarity regions.
• Pathway and disease research: Analyze conserved subnetworks and complexes involved in biological processes relevant to disease research and therapeutic development.

Methodology:

PINALOG combines sequence similarity (via PSI-BLAST), functional annotations, and topological data to map equivalent regions in PPI networks, revealing conserved pathways and interactions.