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Theory and implementation

This analysis is based on an analytical relationship for the estimation of the generalized order parameter $S^2_i$ (see Section 4.2.7.1) of N-H vectors of the protein backbone. It related $S^2_i$ of the N-H vector of residue i to close contact experienced by the H atom and the carbonyl oxygen of the preceeding residue i-1 with heavy atoms k using the formula:
\begin{displaymath}
S^2_i(t) = tanh\left(2.656\sum_k \left((exp(-r^O_{i-1,k}(t)))) + 0.8exp(-r^H_{i,k}(t))\right)\right) + b
\end{displaymath} (4.199)

where $r^O_{i-1,k}$ is the distance between the carbonyl oxygen of residue i-1 and heavy atom k and $r^H_{i,k}$ is the distance between the amide proton of residue i and heavy atom k. The parameter b is set to -0.1 which takes into account that order parameters of rigid protein regions typically lie around 0.9. The sum ranges over all heavy atoms k that do not belong to amino acids i and i-1. For more details about this method, please refer to Ref. [73]

Beside the time-dependent $S^2_i(t)$ defined in Eq; 4.199, nMOLDYN also provide a time-averaged $S^2_i$ defined as:

\begin{displaymath}
S^2_i = \frac{1}{N_{frames}}\sum_{i=1}^{N_{frames}} S^2_i(t_i)
\end{displaymath} (4.200)

where $N_{frames}$ is the number of selected frames for the analysis.


next up previous contents
Next: Parameters Up: Order Parameter (Contact Model) Previous: Order Parameter (Contact Model)   Contents
pellegrini eric 2009-10-06