Re: [DIYbio] Re: Molecular Dynamics

On Wed, Oct 31, 2012 at 6:44 AM, Josiah Zayner <josiah.zayner@gmail.com> wrote:
> I was doing some basic MD. I wanted to compare simulations of proteins that
> start from X-ray structures or NMR structures. One would predict that
> because of the nature of crystals that some X-ray structures might simulated
> differently due to starting in unnatural conformation. However, people think
> that X-ray crystallography is the gold standard in structural biology,
> predicting structure &c. when some of these structures are probably
> slightly, majorly off. I need to redo it though actually using NMR and X-ray
> structures from the same proteins instead of different proteins.

Are you saying that sometimes the way proteins crystallize isn't how
they are in situ, and you want to compare many different
crystallization methods with the structures produced to find your way
back to what they're really like in situ? Which you can then compare
with simulations?

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