bharat gupta wrote:
Thanks for your reply..
Actually I came across a paper "Molecular Modeling of the RNA binding
N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in
Solution with Phosphate ion"... This paper was published in 1996, by Dr.
David van der Spoel.. In this paper , they were trying to find out where
exactly the phosphate ions bind to the peptide.
I thought may be I can try this but in their case it was a peptide and I
am dealing with a barrel protein. As u said that I can go for docking
and binding site prediction tools.. Since I am having some of docked
complexes of my protein with phosphate ion, can I use MD for checking
how strong the binding is or does the ion tries to move inside the barrel.
It sounds like steered MD and umbrella sampling would be useful. You can pull a
phosphate ion through the channel if that's of interest. Otherwise, you can
pull the phosphates from whatever binding sites you've determined to get free
energy changes for any of these processes.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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