6 replies [Last post]
Maxorz's picture
User offline. Last seen 5 years 31 weeks ago. Offline
Joined: 07/16/2009
Groups: None

I've been playing this game for about a week or so, and I just found out through twitter about this: http://newscenter.lbl.gov/press-releases/2009/07/20/fast-protein-structures/

So, it's about a new process that has been created @ Berkeley, which is able to reveal the protein structures much faster than the methods used before... And I was just wondering if this will have any impact on the game... Are we, mortal beings, now going to have to defeat also this powerful mechanism?! :P Fun!!

Haha, but really, how could this effect the project? If in any way.

admin's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 11/10/2007
Groups: vi users
Not really

In a word, no.

In a bit more detail, though not as a biochemist, this breakthrough is about determining the structure of crystallised proteins in the lab. Foldit is about modelling proteins in software, which can then get tested through the lab, but the work is really in software. The two approaches are different, because crystallography is not applicable to all proteins, it doesn't help with design, and crystal structures are different in various small ways from true native structures, which we try to model. Last of all, the idea of Foldit itself can, and I hope will be, applied to other avenues of scientific research.

Joined: 05/09/2008
Groups: None
exciting result, but more work needs to be done!

Thank you for posting this as it is an exciting result.

If indeed they could solve many unknown protein structures, it would help Rosetta in that we would have more fragments from real proteins to use! This would directly help Foldit as it would make the Rebuild tool more powerful.

The main limitation with SAXS is:

"X-ray crystallography yields extremely high-resolution images, while small angle x-ray scattering yields a protein’s shape at a much lower resolution of about 10 angstroms (one angstrom is one ten-millionth of a millimeter)."

So currently, SAXS doesn't yield results that are as accurate as x-ray crystallography or even nuclear magnetic resonance.

That doesn't mean that it doesn't have the possibility of being useful, for example we could use the data from SAXS to help guide Rosetta, eliminating predictions that don't agree with the SAXS data.

But as was posted above, this will not effect Foldit... at least not yet!

Maxorz's picture
User offline. Last seen 5 years 31 weeks ago. Offline
Joined: 07/16/2009
Groups: None
Oh, hehe :P

Oh haha, thanks ^_^ I was just wondering :P To be honest, I'm still learning about all of this protein folding and biochemistry in general, and I can't completely understand many things and what they have to do with each other ... Thanks!

Joined: 05/09/2008
Groups: None
no problem!

Thanks for posting that recent article, I hadn't come across it yet and it led to a lively discussion in lab yesterday!

Joined: 09/27/2009
Groups: None
help with adding images


I tried to add image but I don't know how to do this
Can anyone be kind to tell me how?

thanks a lot

Joined: 05/09/2008
Groups: None
how to post an image

Just underneath the textbox where you type in your comments is a little icon (just above the "Input format" box)

It looks like a green PLUS sign on top of a small photo.

Click on that and you should be able to post an image!


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons