Yes, larger motions have some influence as far as the binding site is in the interface of homodimer and there are some little oscillations in monomers distance. But I actually also want to optimize somehow the number of clusters.
04.12.09, 12:20, "Thomas Cheatham III" <tec3.utah.edu>:
>
> > I actually want to divide trajectory of 5000 snapshots from 5
> > nanoseconds into 10-20 representative structures as it is done in
> > relaxed complex scheme, but in my case i dont have a ligand, just want
> > to simulate the protein flexibility by usage of most common structures
> > with rigid docking. So what procedure is best for such a purpose and is
> > there anywhere more detailed description of these procedures?
>
> What I would do, if trying to select structures for docking is come up
> with a list of active site residues, and then cluster to these... Let's
> assume the active site is residues 10,11,15,20.
>
> cluster out reps20 representative pdb average none all none averagelinkage \
> clusters 20 mass rms :10,11,15,20
>
> If you are concerned about larger motions of the entire protein use all
> protein residues...
>
> -- tec3
>
>
>
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Received on Sun Dec 06 2009 - 04:30:03 PST
