Article ID: 184 - Last Modified: December 4, 2010
My initial IFD calculation does not appear to produce the correct binding mode. What can I do to improve the results?
It is possible to increase the sampling of your ligand in the binding site by mutating a small number (1 or 2) of side chains in the initial docking stage to Ala. This is especially useful when you expect these side chains to undergo large conformational changes upon binding of the ligand. These side chains are reintroduced in the binding site in the second stage of the IFD protocol.
Keywords: side-chain, mutation, Ala, IFD
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