CaverDock: Analysis of Ligand Transport through Protein Tunnels

Ondřej Vávra from ICRC

Understanding protein-ligand interactions is crucial for drug design and enzyme engineering. The interaction of protein and small ligand molecule often takes place in protein’s binding or active site. Such functional sites may be buried inside the protein core, and thus transport of a ligand needs to be studied. We present CaverDock tool, implementing a novel method for analysis of transport processes. The method is based on modified molecular docking algorithm of AutoDock Vina. The output is ligand’s trajectory and energy profile of the transport process.

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