ATPdock

ATPdock predicts protein-ATP binding poses using a template-based docking approach to identify and refine protein-ATP interactions for structural biology and drug discovery.

Key Features:

• Blind Docking Capability: Operates without predefined binding-site specification, enabling docking when binding-site information is unavailable.
• Template-Based Approach: Leverages a database of pocket-ligand structures to identify template pockets and corresponding ligands resembling the query protein pocket.
• Automated Pocket Identification: Uses ATPbind to predict the most likely ATP-binding site when no pocket is provided.
• Structural Alignment Tools: Employs APoc for pocket structural alignment and LS-align for ligand structural alignment to align the initial ATP pose (rdATP) with the template ligand.
• Energy Optimization: Refines docking poses via Metropolis Monte Carlo simulations guided by the AutoDock Vina energy function.

Scientific Applications:

• Drug Discovery: Supports identification and analysis of protein-ATP interactions relevant to therapeutic targeting.
• Structural Biology: Facilitates structural interpretation of protein-ATP binding modes and exploration of novel ATP-binding sites.

Methodology:

For proteins without a defined pocket, ATPbind predicts ATP-binding sites; APoc searches a database of pocket-ligand structures to select a template pocket; LS-align aligns the initial ATP pose (rdATP) to the template ligand; Metropolis Monte Carlo simulations refine the pose using the AutoDock Vina energy function.