The Gaussian network model: Theory and applications

A view that emerges from many studies is that proteins possess a tendency, encoded in their three-dimensional (3D) structures, to reconfigure into functional forms, that is, each native structure tends to undergo conformational changes that facilitate its biological function. An efficient method for identifying such functional motions is normal mode analysis (NMA), a method that has found widespread use in physical sciences for characterizing molecular fluctuations near a given equilibrium state. The utility of NMAas a physically plausible and mathematically tractable tool for exploring protein dynamics has been recognized for the last 20 years [1, 2].With