  A simple way to get insights about the possible functional motions of a
protein is to perform a normal mode analysis (NMA). Indeed, it has been shown
that low-frequency modes thus obtained are often closely related to domain
motions involved in protein function. Moreover, because protein low-frequency
modes are known to be robust, NMA can be performed using coarse-grained models.
As a consequence, it can be done for large ensembles of conformations as well
as for large systems, like the ribosome, whole virus capsids, etc.
Unexpectedly, on the high-frequency side, modes obtained with cutoff-based
coarse-grained models also seem able to provide useful insights on protein
dynamical properties.
