How about including biopolymers?
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Profile Michael H.W. Weber
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Message 338 - Posted: 17 Jul 2017, 6:32:24 UTC
Last modified: 17 Jul 2017, 6:45:52 UTC

As far as I have understood, so far, this project is focusing on data from this database which excludes biopolymers (such as proteins, DNA and RNA).

My question is: Given todays general importance of biotechnology and, more specifically, knowledge of biomolecules, wouldn't it be possible to also include proteins, RNA and DNA at a later stage in this project by using data supplied here (or elsewhere)?

And if so, how much more complex would the calcualtion be (future average WU duration compared to todays average WU duration on GPUs)?

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Michael.
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Message 339 - Posted: 17 Jul 2017, 12:24:32 UTC - in response to Message 338.

As far as I have understood, so far, this project is focusing on data from this database which excludes biopolymers (such as proteins, DNA and RNA).

My question is: Given todays general importance of biotechnology and, more specifically, knowledge of biomolecules, wouldn't it be possible to also include proteins, RNA and DNA at a later stage in this project by using data supplied here (or elsewhere)?

And if so, how much more complex would the calcualtion be (future average WU duration compared to todays average WU duration on GPUs)?

Best regards,
Michael.

That's a good question! If the positions of atoms in the protein molecule are known along with the unit cell properties of the crystal structure, there are no technical difficulties to calculate the powder diffraction pattern of this protein. However, for the nanocrystals of proteins, these patterns are barely informative or non-informative at all, because multiple diffraction peaks of finite width overlap each other (the more complex the molecule is the more peaks will be on its diffraction pattern).

A common approach in the study of proteins' structure includes the following steps:

1) growing a good quality microcrystal (not a nanocrystal) of the protein (this is a hardest step),
2) measuring multiple diffraction patterns (single-crystal not powder) for different mutual orientations of the protein's monocrystal and the incident beam of photons (x-ray), neutrons or electrons.
3) iterative refinement of the protein's structure using the measured single-crystal diffraction patterns (there are a lot of software aimed at this problem).

Unlike the one-dimensional powder diffraction patterns, which are obtained for the powder samples where the orientations of the crystals are random, the single-crystal diffraction patterns are two-dimensional. When you have a bunch of them, they provide much more information on the structure than a powder diffraction pattern.

There is a research showing that for some proteins you can replace the step 2 with measuring the powder diffraction pattern, however, the step 1 cannot be replaced, you still need a good quality microcrystal. But for the microcystals there is no need to calculate the powder diffraction using the general Debye equation which we are doing in this project for the nanocrystals.

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Message 340 - Posted: 17 Jul 2017, 15:51:00 UTC - in response to Message 339.

There is a research showing that for some proteins you can replace the step 2 with measuring the powder diffraction pattern, however, the step 1 cannot be replaced, you still need a good quality microcrystal. But for the microcystals there is no need to calculate the powder diffraction using the general Debye equation which we are doing in this project for the nanocrystals.


It's a pity. I like protein folding research! :-)

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