accelerated MD as the engine for loop refirement

From: James Starlight (
Date: Wed Jul 09 2014 - 14:39:08 CDT

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?



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