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Maximum Likelihood Trajectory
This site provides tools for calculating the most probable trajectory between two known structures, in the sense of maximum Likelihood as defined by Onsager and Machlup (1953).
The program has been written by Joel Franklin (Franklin et al., submitted) and works under the general assumption that the Energy lanscape around each (initial and final) state is harmonic; here we use the Elastic Network Model due to M. Tirion (1996).
In this case, the problem can be solved exactly analytically. The crossing point between the two multi-dimensional potential energy curves is found iteratively by the program in a simple 1D search which imposes continuity of the Energy on both sides of the transition.
For the moment the program only handles structures with CA only.
Once the trajectory has been obtained, the movie can be played with PyMol or VMD directly.
The CA coordinates of the intermediates along the pathway can also be used to reconstruct the full protein using another option of this web site (due to Patrice Koehl).
Page last modified 13:05 April 11, 2007.