Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
Fig 3
Final configurations of the four models of the VSD with different molecular fragments.
The final configuration (left panel) and the correlation between the Cβ-Cβ distance and the Sγ-Cd2+, Oδ2-Mg2+, Nε-Zn2+, or Nζ-Oε2 distance in each molecular fragment (right panel) of (A) model-1, (B) model-2, (C) model-3, and (D) model-4. The last 10 ns trajectories of the restrained MD simulations were used to calculate the average values and standard deviations of the distances.