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Message boards : GPUGRID CAFE : How accurate is the simulation of a protein?

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Dave
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Message 38847 - Posted: 6 Nov 2014 | 9:22:19 UTC

Hi there,

I've recently joined GPUGrid, mainly because I was looking for a project, that was able to utilize my GTX 980 more than Einstein@Home can do (due to old Cuda version).

So I looked at the initial intro video at the website in which the researches were talking about the protein and how a drug would interact with it.

The first thing that came into my mind was: How accurate is the simulation? And are the conclusions drawn accurate?
I'm an electical engineer student and I've have run multiple simulations myself on electric field behavior in vacuum interrupters. Different story, but from my experience I know that it's easy to generate "nice graphs" but what about reality? How do you verify your simulations?
Does this model you are using really help to unterstand the interaction and develop new medication?

Thanks in advance,

David

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Message 38852 - Posted: 6 Nov 2014 | 10:40:45 UTC - in response to Message 38847.
Last modified: 6 Nov 2014 | 10:41:59 UTC

Good questions!
It's tricky to validate the accuracy of the simulations considering that there is no experimental technique that can do the exact same thing MD (molecular dynamics) does, in the sense of time and space resolution.
However we can and have validated our results on various experimental data such as protein crystal structures, NMR data (see Nate's publication) and various other experiments.

It has been shown in various papers that it is possible to fold proteins with MD simulations to their native structure seen by Xray crystallography. However as MD simulations are still quite slow, we can only validate this on relatively small and fast-folding proteins. So for all we know, the current MD force-fields might for example not be able to fold huge proteins.

Noelia is also about to publish a paper where she does protein-ligand simulations and then validates the results of the simulations to experimental results with quite good success.

So in general I would say that over the last years the accuracy of the simulations has increased a lot and can be used to partially replace some experiments, or at least be used as an extra tool in drug design, which is also what we are trying to sell to the public :)

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Message 39030 - Posted: 26 Nov 2014 | 21:32:56 UTC - in response to Message 38852.

...or at least be used as an extra tool in drug design, which is also what we are trying to sell to the public :)


Can you provide more detail about this comment? What exactly is being sold to whom?

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Message 39037 - Posted: 28 Nov 2014 | 4:27:15 UTC - in response to Message 39030.

...or at least be used as an extra tool in drug design, which is also what we are trying to sell to the public :)


Can you provide more detail about this comment? What exactly is being sold to whom?


I think that by "sell to the public" he means "convincing the public" (getting the public buy their story of how GPUGRID is doing cutting-edge research blah blah) to donate their computational power to the project.[/i]
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Message 39038 - Posted: 28 Nov 2014 | 9:36:34 UTC
Last modified: 28 Nov 2014 | 9:37:40 UTC

What Chilean said. I meant "selling to" as "convincing someone". But not just crunchers for our project. We also want to convince the industry that it can be useful for real drug design applications. Most pharma companies are still a bit behind computationally, or at least are being a bit conservative about entering this field.

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Message boards : GPUGRID CAFE : How accurate is the simulation of a protein?