I have docked some chemical probes into my enzyme of interest Using CB-Dock2 services. I get multiple cavities detected but i know the one i want to dock in so only select 1 cavity. then it produces a protein-ligand complex when docking is complete.
However it only shows me one possible pose for the docked ligand in each cavity. Is there a way to be able to view multiple binding modes/poses in the same cavity? I tried downloading the protein-ligand complex pub and the ligand mol2 file but cant seem to find where to see other options for the same cavity? I was told there were multiple options for each cavity and it is possible to view them but i am unsure.
Few ligand docking software allows you to explore multiple poses for a given ligand in a specific binding site. While CB-Dock2 might not provide this feature directly, you can try other docking tools like AutoDock or GOLD, which allow for flexible ligand docking and can provide multiple poses.
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