Dear B.Nataraj,
> For my modelled protein, I want to analyis various possible > conformare it can assume,In that connection I want to know what is the > command or in build routine to create all possible conformation for > my modelled protein ? Thank you in advance.
To analyze possible conformers avalible to your model, you can run a molecular dynamics simulation with implicit or explicit solvent. On the latter case you first add a water shell to your model and minimize just the water shell, and after that you minimize the water-protein assambly. Finally you run a looooooooong dynamic, sample conformations at regular intervals of the simulation and voila!! You now have several conformers of your model!!
You can do a search on NCBI Pubmed to get more info on this (software, parameters, etc). As always, what you do is defined by your needs and the computing resources available to you.
I hope this helps,
Kind regards, Luis.
On Sunday 11 April 2004 19:52, Nataraj Balkrishnan wrote: > > For my modelled protein, I want to analyis various possible > > conformare it can assume,In that connection I want to know what is the > > command or in build routine to create all possible conformation for > > my modelled protein ? Thank you in advance.
On Monday 12 April 2004 22:57, Luis Rosales wrote: > To analyze possible conformers avalible to your model, you can run a > molecular dynamics simulation with implicit or explicit solvent. On the > latter case you first add a water shell to your model and minimize just the > water shell, and after that you minimize the water-protein assambly. > Finally you run a looooooooong dynamic, sample conformations at regular > intervals of the simulation and voila!! You now have several conformers of > your model!!
In fact, given Luis Rosales suggestion to do "a looooooooong molecular dynamics", you could use normal mode analysis as a fast tool to obtain different conformations of your protein. Our NMA web server ElNemo
http://igs-server.cnrs-mrs.fr/elnemo/
allows you to generate normal mode perturbed states of your protein (i.e. look ate the "example" page). We have shown this to be a way to solve difficult molecular replacement problems in X-ray crystallography (if that is what you need the models for).
Kind regards, Karsten.
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Karsten Suhre -
Luis Rosales