Re: [AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral)

From: David A Case <>
Date: Wed, 21 Dec 2016 08:02:47 -0500

On Wed, Dec 21, 2016, Trang Nguyen wrote:
> I am trying to study ensemble conformations of a free enzyme (626 residues)
> by MD starting from its xray structure in the bound state with a substrate.
> There are also some NMR data of the free state enzyme (RDC, dihedral) but
> not fully recorded since the free form is quite flexible.
> Could you please suggest me any idea/ literatures to start with? The
> problem is how to make use of NMR data to support enhanced sampling
> conformations with such a large system.

You could look at papers from Martin Blackledge, who has written a lot about
interepreting RDC's and other NMR data for flexible systems. Ordinarily, one
would use enhanced sampling of various sorts (all will be extremely difficult
for a 600-residue polypeptide), and then use RDC's to assess the resulting
ensemble. Work by Vendruscolo, trying to create the ensembles, is also worth
consulting. But if you have data that is "not fully recorded", and a very
large system, the NMR data is probably not going to be very helpful.


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Received on Wed Dec 21 2016 - 05:30:03 PST
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