Similarity measure and order parameter

In order to verify the structural similarities of two conformations X = (xi, X2. x r) and X = (x l, Xj. X ), the most frequently used standard measure is the root mean square deviation (rmsd) of the respective stmctures, 

Another, less costly, unique alternative is the introduction of an angular overlap order parameter. Before we define it, let us first discuss the characteristic features of free-energy landscape parametrized by angular degrees of freedom. 

Definition of the torsion angle which is defined as the angle between the two planes spanned by the monomers /, 

Exemplified bond and torsion angle distributions of seguence/l4fi22l452l262l3622l at different temperatures. The distributions ofthe torsion angles are reflection-symmetric and therefore only the positive intervals are shown. From [47], 

Protein folding channels and kinetics of two-state folding 

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