I2I-SiteEngine

I2I-SiteEngine compares protein-protein interfaces by evaluating physicochemical properties and three-dimensional shapes to identify analogous interaction regions.

Key Features:

• Interface comparison: Compares protein-protein interfaces extracted from complex structures to detect local interface similarity.
• Physicochemical and geometrical similarity: Recognizes local geometrical and physicochemical similarities between interacting binding sites, enabling detection of functional analogs independent of sequence homology.
• Three-dimensional alignment: Computes the three-dimensional transformation that maximizes similarity between pairs of interacting binding sites.
• Input and output: Accepts two protein-protein complex structures as input and outputs a superimposition in PDB file format plus a detailed list of shared physicochemical properties.
• Efficiency and scalability: Implements algorithms optimized for large-scale database searches across the Protein Data Bank (PDB).

Scientific Applications:

• Functional prediction: Infers potential functional similarities by identifying conserved interface physicochemical and geometric patterns.
• Drug discovery: Identifies similar interaction sites to prioritize novel binding sites or targets for modulation of protein-protein interactions.
• Protein engineering: Guides modification or redesign of interfaces by revealing analogous interaction regions and shared physicochemical features.

Methodology:

Extracts interfaces from input protein-protein complex structures and finds the three-dimensional transformation that maximizes similarity between pairs of interacting binding sites through detailed comparison of physicochemical properties and spatial configurations.