Dear Ananya,
Shouldn't this be something you already had in mind even before attempting
to simulate? Usually, a simulation is a means to an end. What is your end,
ie. what made you do this simulation? The motivation behind your simulation
is usually what will determine what type of validation it
On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote:
Dear Ananya,
Shouldn't this be something you already had in mind even before
attempting
to simulate? Usually, a simulation is a means to an end. What is your
end,
ie. what made you do this simulation? The motivation behind your
Dear Ananya,
Sorry but I don't understand what you're saying. What do you mean by molecular
movement of my protein? Do you mean diffusion? Please be more specific.
You also mention authenticity, but I don't think that's what you meant...
You have done PCA, RMSD and RMSF analyses. That's nice and
Dear Sir,
My protein contains two domain and upon GTP hydrolysis, the protein
under goes conformational change and it shows inter-domain movement. I
did few biochemical test which showed me that the upon a mutation in the
conserved residue (which is localed in the chain connecting the two
First of all, please address me in a casual manner, Sir makes me feel old
and I'm just in my mid 20's :)
Now I'll try to be as less verbose as I can, because I think there's a
little communication issue here.
Authenticity usually points out towards originality, something not copied,
genuine. I
Hi Ananya,
You have several options to validate the results you have
1. Perform the simulations again
2. Apply the reverse mutations and simulate again
3. Perform (covariance) analysis on different blocks
4. Extract a measurable property and compare it to experiments
ad 1.:
Redoing the
Well,
I also would check which kind of movements I am looking for. It is a known
fact that some domain (and, thereby, larger) movements occur in larger
timescales and that might not be your case.
E.g: you are expecting to see major movements in nanoseconds timescale.
I hope this helps.
Best
On 2/11/14, 6:43 AM, ananyachatterjee wrote:
Dear Sir,
My protein contains two domain and upon GTP hydrolysis, the protein under goes
conformational change and it shows inter-domain movement. I did few biochemical
test which showed me that the upon a mutation in the conserved residue (which
Hello everyone,
I have done a set of molecular dynamic simulation of my protein and its
mutated structure, now please tell me how should I validate the
simulation results or structures. Whether I can reproduce the same
simulations.
Thank you in advance
--
Ananya Chatterjee,
Senior Research
