Dear Mahesh,
In addition to RMSD plots, you could try to quantitatively analyse the
protein residue flexibility in order to detect backbone conformational
transitions by means of the method proposed in:
Local Fluctuations and Conformational Transitions in Proteins
Rocco Caliandro, Giulia Rossetti, and Paolo Carloni
J. Chem. Theory Comput. 2012, 8, 4775−4785
By starting from a set of several models of the same protein, the
method allows to detect the "hinge points" of the protein and the
residues where transitions between two different conformational states
occur.
However, by inspecting your picture, also I am not convinced that they
are alterations of the protein, but rather inconsistency in assignment
of secondary structure.
Danilo
