[gmx-users] Re: Reg: Validation of Protein-Protein Interaction through simulation

[Amit]

Dear Dr. Lemkul,
                         Many thanks for the reply and suggestion. I
believe doing docking first and then going for simulation is more
relevant as this will lessen the nonspecific interaction. Correct me
if I am wrong. Also I would like to ask one more question. I would
like to simulate gold nanoparticle and protein together. So how can i
prepare the .pdb and topology file for the nanoparticle as it is
composed of charged atoms? Please let me know.

On Thu, Mar 21, 2013 at 4:42 PM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5006519h62 at n6.nabble.com> wrote:
>
>
> 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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-- 

Yours Sincerely,

~~~~~~~~~~~~~~~~~~~~~~~~
Amit Jaiswal,
Department of Bioinformatics,
School of Life Sciences,
Pondicherry Central University,
Kalapet, Pondicherry,
Puducherry - 605 014.
Phone No.: +91 8124954834.

~~~~~~~~~~~~~~~~~~~~~~~~~




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