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We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking (involving both small and large conformational changes for the complex), which are the most useful hydrodynamic techniques? If not hydrodynamic, which others?

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NMR would be a method to get structural and dynamics information, but that is not a quick and easy method. Are you looking for atomic-resolution data, or for simpler methods that only give you some global information on the shape and dynamic of the protein? – Mad Scientist Oct 5 '12 at 21:26
    
I am interested in both, atomic resolution data, and/or "coarse grain" model data – flow Oct 7 '12 at 8:32

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