On 3/21/13 5:11 AM, Amit wrote:
Dear Gromacs Users,
I am new to gromacs software and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each other by co-immunoprecipitation techniques. Is there a
way out to know weather protein A really interacts with B through
simulation? Is it possible to simulate both the proteins together in a
single box without doing docking? Can simulation provide the interacting
regions? I want to incorporate both the proteins together in box without
docking. Please correct me if I am wrong.
Depending on the size of the proteins, doing an unbiased simulation of
protein-protein binding may or may not be feasible. There is a high probability
of nonspecific interactions, which may or may not be relevant. If you bias the
simulation towards interacting in some preconceived way, then the simulation
doesn't show much more than the fact that it did what you told it to do.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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