Re: Determining Transition State from an Unfolding Simulation

From: Neelanjana Sengupta (
Date: Sun Sep 23 2007 - 18:33:44 CDT


This would work (if at all) assuming your unfolding pathway retraces the
protein folding pathway. If you figure out a way to determine if this is
what is going on (figuring this out would indeed be non-trivial), you may
then closely examine the timeline of a unfolding parameter (Rg, for
instance) and see if it is stable over an extended period of time. If you
find that the energy is stable too, then you "may" think that you have
encountered a transition state. However, a lot of caution is required in
your treatment...

Would be great if others share their thought too!


On 9/23/07, Arun Krishnan <> wrote:
> Hi All,
> Is there a way to calculate the transition state structure from Unfolding
> data? From the plot of RMSD vs time maybe?
> Or is there some other way? Any pointers would be much appreciated.
> Cheers,
> Arun


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