Small protien folding?

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Small protien folding?

Postby TheMageKing » Wed Apr 20, 2016 3:30 pm

I understand that folding@home has bypassed the millisecond barrier, is able to handle proteins made of thousands of amino acids. But what about smaller proteins that take longer to fold? I think such proteins should be folded to expand knowledge. If we increase the number of proteins folded, we can build analytical data to help speed folding and prevent errors. So is folding @home doing this? If not, why not?
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Re: Small protien folding?

Postby 7im » Wed Apr 20, 2016 5:26 pm

Hello TheMageKing, welcome to the folding forum.

The Folding@home project has been running for more that 15 years, which means that when it first started, a Pentium II was a powerhouse. The project didn't have a choice but to fold small proteins, and has pretty much folded as many small proteins as needed. The first five years of the project spent a great deal of time building analytical data to increase the accuracy of the folding cores and eliminating errors, aka, expand knowledge of folding proteins. The second five years had a focus to increase speed so we could get meaningful results is a much shorter time, which also allowed the project to work on larger more interesting proteins.

So technically, no, Folding is no longer working on small proteins just for the sake of increasing it's general knowledge about folding proteins. That is no longer necessary. However, the size of a protein studied has much less to do with the selection of which proteins are studied as what the function of the protein does in relation to how it impacts a disease or illness. Folding@home would fold small proteins if needed to study a disease, but not for the sake of expanding general knowledge. Plus, smaller proteins do not typically take longer to fold in (vitro/in vivo) than larger proteins.
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Re: Small protien folding?

Postby bruce » Wed Apr 20, 2016 6:09 pm

Larger proteins work better on GPUs and on systems which are folding with a lot of CPUs.

If there happen to be small proteins or small segments of larger proteins that need to be folded, they're typically assigned to systems which are folding with a low CPU count.
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