Re: [modeller_usage] How to get various conformar for a modelled protein?

[Karsten Suhre <>]

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.