On Mon, Oct 18, 2010, Sangita Kachhap wrote:
>
> I want to calculate binding affinity of two protein to its cognate DNA i.e.
> binding affinity for a protein bound its
> cognate DNA and then binding of second protein which seems to increase the
> binding affinity of first protein to DNA to above complex.
>
> Can I use MD simulatiion here to calculate it?
> Is AMBER usefull for it if yes then which module?
This is likely to be an almost impossible calculation, at least in any
straightforward fashion. It would certainly be a significant research
problem to try to gain understanding of this sort of cooperative behavior.
You would certainly want to become comfortable with calculations of
binding of single proteins to DNA, where good structural models are
available, prior to trying a more difficult problem. The usual advice
holds: see if there is some paper in the literature that describes
a computational approach to something similar to the problem you have in mind.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 19 2010 - 03:00:03 PDT
