Assessment of ab initio models of protein complexes by molecular dynamics
Fig 1
Root-mean-square deviation from the position of Cα atoms in the respective models of G3:HER2_IV complex as a function of simulation time.
While some models rapidly move away from the initial pose, others only deviate from the initial structure when temperature is increased. The only model that even after 20 ns simulation at a temperature of 390 K remains close to the initial structure is model r37, that is, the one closest to the correct structure.