AMDock

AMDock performs protein–ligand docking workflow orchestration by integrating AutoDock Vina and AutoDock4 (including the AutoDock4Zn force field), preprocessing tools, and PyMOL visualization to support docking studies and ligand selectivity analyses.

Key Features:

• Integration with AutoDock Vina and AutoDock4: Executes docking with AutoDock Vina and AutoDock4 and supports the AutoDock4Zn force field for metalloprotein studies.
• Comprehensive workflow support: Uses Open Babel and PDB2PQR for structure preparation and employs AutoLigand and ADT scripts to define the search space.
• Visualization with PyMOL: Uses PyMOL for molecular visualization, docking-box setup, and analysis of docking results.
• Off-target docking procedure: Implements an off-target docking workflow to enable ligand selectivity and potential off-target interaction analyses.

Scientific Applications:

• Drug Discovery: Facilitates protein–ligand docking studies to identify and optimize potential drug candidates.
• Protein Engineering: Enables exploration of protein–ligand interactions to inform engineered protein design.
• Metalloprotein Studies: Supports specialized docking studies of metalloproteins using the AutoDock4Zn force field.

Methodology:

Automates preparatory steps and integrates Open Babel and PDB2PQR for input preparation, uses AutoLigand and ADT scripts to define the search space, runs AutoDock Vina and AutoDock4 (with AutoDock4Zn option), employs PyMOL for visualization, and implements an off-target docking procedure.