I would like to add a ligand to the active site of my structure and then refine the loop around it or optimize only the side chains. Can I do this in Prime?

Yes, you can include the ligand and refine the loop or the side chains around the ligand. As always, ensure that your ligand and protein are properly prepared first. It is a good idea to request more than the default 5 loops as output from the Prime loop refinement. Side chains are minimized as part of the refinement, so you don't need to do a separate side-chain prediction after the loop refinement.

Keywords: Prime, loop refinement, ligand

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