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724: Blind Electron Density Puzzle 7
Status: Closed


Name: 724: Blind Electron Density Puzzle 7
Status: Closed
Created: 06/03/2013
Points: 100
Expired: 06/11/2013 - 07:00
Difficulty: Advanced
Description: This Electron Density puzzle is going to be as difficult as they get! Why? Because the automated methods for fitting electron density were unable to solve this structure using this density. But where computers fail, Foldit players triumph! Use all your Electron Density folding skills to fit the density as well as you can. As requested in the last Scientist Chat, we have added secondary structure predictions onto the starting model, with more details posted in the puzzle comments.
Categories: Electron Density, Overall, Prediction

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Joined: 05/09/2008
Groups: None
Here are the secondary structure predictions!

As requested in the last Scientist Chat , here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Valines at residues 7, 121 & 128 are predicted to be part of a sheet. However, the Valines at residues 36, 91, 102, 113 & 141-142 are highly predicted to be part of a helix!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).

Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.

bertro's picture
User offline. Last seen 8 weeks 11 hours ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Just kidding

Are you sure there is at least one copy of the protein in this cloud?

Joined: 05/09/2008
Groups: None

at least there are helices in there somewhere, right? ;-)

bertro's picture
User offline. Last seen 8 weeks 11 hours ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Right !


Madde's picture
User offline. Last seen 1 year 14 weeks ago. Offline
Joined: 05/29/2008
Groups: Void Crushers
Picking some nits

I just noticed this is actually the 7th Blind ED puzzle, the 6th one was puzzle 666: http://fold.it/portal/node/994258

Joined: 05/09/2008
Groups: None
nice catch!

I got caught by "Blind Electron Density Puzzle 5 Round 2!" being after ED 6


alwen's picture
User offline. Last seen 6 days 4 hours ago. Offline
Joined: 10/03/2011


Not a lot of big hydrophobics in this one to use for landmarks, just that tryptophan at 80 to align the big helices.

It's possible the cloud is cut so we have the small helix from another copy.

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