HawkDock

HawkDock predicts and analyzes protein-protein interaction three-dimensional structures to identify binding conformations and key interface residues.

Key Features:

• ATTRACT docking algorithm: Performs initial prediction of protein-protein complex structures using the ATTRACT docking algorithm.
• HawkRank scoring function: Re-scores and refines docking models using the HawkRank scoring function developed by the HawkDock group.
• MM/GBSA free energy decomposition analysis: Applies MM/GBSA free energy decomposition to quantify per-residue contributions and highlight key interface residues.
• 3Dmol.js molecular visualization: Provides molecular visualization of predicted PPI structures via 3Dmol.js.
• Performance benchmarking: Reported identification rates compared to ZDOCK 3.0.2 are approximately 81.4% for predicted models and 95.4% for crystal structures.

Scientific Applications:

• Structural biology: Models protein-protein complexes and identifies interface residues to support mechanistic studies of molecular interactions.
• Drug discovery: Informs design of inhibitors or modulators targeting specific protein-protein interfaces by locating binding conformations and key residues.

Methodology:

Initial docking is performed with ATTRACT and re-scored with HawkRank, followed by MM/GBSA free energy decomposition analysis to identify key interface residues.