Treekin

The program treekin (Wolfinger et al., 2004) computes folding dynamics based on a given rate matrix. Usually, it operates on coarse grained versions of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers –rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix).

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References

2004