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Folded proteins change their conformation in varying degrees, ranging from simple pocket breathing to large rearrangements of entire domains, like the spike protein of some viruses. While crystal structures can help enormously understanding your target, they only offer a static picture, a small well of the conformational landscape of your target.

There are many great and fast docking software solutions to predict the binding mode of a ligand to its target. However, in some scenarios, like those where water molecules or protein flexibility play a key role, docking software can fail to predict reasonable poses.