SeamDock

SeamDock performs molecular docking of small compounds to analyze protein–ligand interactions for drug-discovery and research purposes.

Key Features:

• Small compound molecular docking: Performs docking of small compound ligands against protein receptors.
• Integration of docking tools: Integrates various docking programs within a unified framework.
• Global and local docking: Supports both global and local ligand docking approaches.
• Hierarchical strategy: Implements a hierarchical strategy to streamline interaction-site identification.
• Seamless framework and RPBS server: Uses the Seamless framework to link computations to the RPBS calculation server.
• 3D visualization: Provides 3D visualization of ligands, receptors, docking poses, and their interactions.
• Session sharing: Enables sharing of complete docking sessions including associated visualization states.

Scientific Applications:

• Drug discovery: Integration into standard pipelines for drug discovery and candidate evaluation.
• Protein–ligand interaction analysis: Assessment and interpretation of docking poses and inter-molecular interactions.
• Education and training: Use in teaching and training molecular docking techniques and interpretation of results.
• Collaborative research: Support for collaborative projects via shared docking sessions and visualization states.

Methodology:

Integration of multiple docking programs; support for global and local docking; a hierarchical site-identification strategy; computations linked via the Seamless framework to the RPBS calculation server; and 3D visualization of docking poses and interactions.