Figure 2
(A) The comparison of the Cα RMSD distribution of the structures generated by MSA-MD and SSA-MD. Black represents structures from 10 ns MSA-MD; red, blue and grey represent structures from the single trajectory of 2.pdb, 19.pdb, 102.pdb respectively. The Cα RMSD of 2.pdb, 19.pdb, 102.pdb relative to the 1AL1 crystal structure is 1.195 Å, 3.882 Å, 5.085 Å respectively. (B) The comparison of the potential energy distribution of the structures generated by MSA-MD and SSA-MD. (C) Secondary-structure-forming tendencies of the ALPHA1 as a function of residue number. The results are mean values over the final 1000 structures from 10 ns MSA-MD. Square with black solid line: alpha helix structure (H); circles with red solid line: 3-helix structure (G); up triangles with blue solid line: hydrogen bonded turn (T); down triangles with grey solid line: bend structure (S).
