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.