RMSD (for Cα atoms) from the reference experimental structure as a function of time along simulations at 303 K for the G3:HER2_IV complex.

Abstract

<p>Simulations starting from model r37 or from the experimental structure explore a narrow range of conformations close to the experimental structure. The simulation starting from model r44 converges to the correct structure after about 50 ns, suggesting that, despite the remarkable structural difference from the correct structure, model r44 is within the native basin of the free energy surface. All the other trajectories do not lead to the correct state after 32 ns simulation. A simulation started from the experimental structure is also shown: the RMSD fluctuates around 1 Å indicating high rigidity of the complex.</p

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