Apparent stiffness

It is defined as the force-constant acting between two residues in the case of completely disconnected oscillators. It is defined in the harmonic limit from the variance in the inter-residue distance:

$K_{ij}^{app}=\frac{k_BT}{\left<\left(R_{ij}-\left<R_{ij}\right>\right)^2\right>}$

(1)

where k_B is the Boltzman’s constant and T is the temperature. The averages are computed using ensemble computed from either DMD, BD or NMA-based Monte-Carlo simulations.

The index helps to detect strong interactions between residues, which might indicate physically-intense direct contacts or strong chain-related interactions.

Apparent stiffness is indicated as a 2D NxN plot. The exact value of the apparent stifness can be recovered by placing the mouse over the appropriate position of the graph. When more than chain is onvoled in the study, chain boundaries are indicated with black lines in the graph.