Re: accelerated MD as the engine for loop refirement

From: Ajasja Ljubetič (
Date: Wed Jul 09 2014 - 15:22:15 CDT

Perhaps Rosetta <>/pyRosetta
<> might be worth a look, as
these even have a dedicated loop refinement protocol.


On 9 July 2014 21:39, James Starlight <> wrote:

> Dear NAMD users!
> I wounder whether the accelerated molecular dynamics might be good
> solution for the loop refirement of models made by means of hoology
> modeling with the teplated which has the low sequence identify in loop
> region? For instance I've just built some models of membrane receptors
> agains receptor with known structures and would like to refine loops by
> some enhansed sampling engine to sample all possible conformation and found
> most propable during short simulation. Does the acceleraed md good
> sollution for such task assuming simulation with implicit solvent with
> restrained all atoms of the helix regions of the refined protein but not
> loops flexible region? What alternatives should I explored also?
> TFH,
> James

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