Foldit vs. UMich Electron Density Challenge

It is rally time! On Thursday, 22 October, we're releasing a special puzzle challenge for the Foldit community based on a structure of a protein recently solved by crystallographers in the Bardwell Lab at the University of Michigan.

We learned that before the team publishes the structure, they are challenging a class of undergraduate biochemistry students to build a model into this unrefined density map. Knowing our community would enjoy a challenge, the lab also has invited Foldit players to participate!

Here's what you need to know going in:

* The full sequence of the protein will be available; however, note that some parts of the protein are disordered and will not occupy any electron density.
* This puzzle is big, at 199 residues.

We have four weeks to develop a protein model that fits this density (the puzzle will close at 1pm ET/1700 UTC 19 November). Can Foldit players outperform the University of Michigan students—or even the crystallographers themselves?

Edit: The puzzle is LIVE!

(Tue, 10/20/2015 - 16:24  |  8 comments)
Joined: 07/21/2013
Groups: Beta Folders
What kind of protein folding software folding tools

What kind of protein folding software do the students and crystallographers use at the University of Michigan use?

spmm's picture
User offline. Last seen 9 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Coot and MoPro?

Not sure if they have wiggle, shake wiggle sidechains equivalents, doubt if they have rebuild. Also if a large part is disorded foldit players will possibly have more useful tools.

beta_helix's picture
User offline. Last seen 4 days 12 hours ago. Offline
Joined: 05/09/2008
Groups: None
You can read the full paper here:

Indeed they used Coot.

You can read their paper here:

http://sites.lsa.umich.edu/bardwell-lab/wp-content/uploads/sites/265/2015/05/PubJuly2014.pdf

or a short article about it here, if you prefer:

http://www.hhmi.org/bulletin/spring-2014/fitting-task

Joined: 09/24/2012
Groups: Go Science
A suggestion

They say: "Horowitz positioned a single amino acid on the map to show where the protein chain started."

This would be a dream for me: if you could give us the starting point in a density puzzle, it would help !

spmm's picture
User offline. Last seen 9 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Don't want it to be too easy Bruno :)

The last ED challenge puzzle: http://fold.it/portal/node/2000180. We didn't get the N terminus in the puzzle, just 3 residues and we added residues and mutated.

In this one it looks like we will get the sequence, so it will be simpler but twice the size with disorded regions which I guess will not be marked.
The tab scrolling and large move tool have been fixed now as well which is great.

Batz's picture
User offline. Last seen 1 week 2 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
almost got it =)

As I want to promote the Foldit players, I will tell you the following

I found out that the disordered regions are in the first 80 amino acids and are flanked with helical segments which fit the ED, the rest sometimes can be identified, sometimes not...

Joined: 09/24/2012
Groups: Go Science
do you mean

that the latest 119 AAs fit into the ED ?

or on the countrary, some of the 80 fisrst fit into the ED, and the remaining 119 are outside?

(btw I'm personally in the clouds, I mean I don't see anything in these clouds)

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
Some questions

I posted some questions about Electron Density Puzzles in Feedback at http://fold.it/portal/node/2001368

If you know the answers, please post them there. Thanks!

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