What essential information can MD simulations provide about a solved experimental structure, such as one from X-ray crystallography, that the static structure itself misses?
Answer
The pathway the system took to reach that state or other relevant, near-minimum energy states
Experimental techniques like X-ray crystallography or NMR capture a single, low-energy state that the molecular system adopted long enough to be physically measured, representing a snapshot in time. Molecular Dynamics simulations serve to complement this data by exploring the kinetic landscape surrounding that snapshot. MD can map out the dynamic pathway the system navigated to achieve that specific experimental conformation, and crucially, it can identify other closely related, near-minimum energy states that the experiment might have entirely missed, offering a much broader view of the functional conformational ensemble.
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