puzzle picture
655: Blind Electron Density 2
Status: Closed

Summary

Name: 655: Blind Electron Density 2
Status: Closed
Created: 11/20/2012
Points: 100
Expired: 11/27/2012 - 23:00
Difficulty: Intermediate
Description: This is our second electron density puzzle with real data. This should be easier than our last density case, since the scientists were able to pinpoint which regions belonged to a single copy. Try to fit the protein into the density to get the best score!
Categories: Electron Density, Overall, Prediction

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Comments

Joined: 08/30/2011
secondary structures

SS would be nice

brow42's picture
User offline. Last seen 1 week 2 days ago. Offline
Joined: 09/19/2011
Groups: None
structures

Susume got a jpred prediction of the structure, which is listed here:

http://fold.it/portal/recipe/44687

brow42's picture
User offline. Last seen 1 week 2 days ago. Offline
Joined: 09/19/2011
Groups: None
Good puzzle

I really liked this puzzle. It had exactly the right amount of detail I need. You could see the backbone and some sidechains. I'm not anywhere near the high score but I think whomever has the high score will have good results for you.

The last blind ED puzzle (on a lattice) was too complicated for me to play, it was just random blobs. Also, the simulated noisy ED in the past were also too noisy to play. But this, despite being noisy real data, is quite playable. I could see sheets and helices clearly in the ED. I'm pretty confident I'm within 1 segment width for my puzzle.

However, I couldn't have done it without Susume's jpred prediction. There are so many ambiguities in denovo folding, starting with "which end is first". I'm sure only the most experienced folders can start without a structure prediction. Sure, it was mostly loops = no preferred structure, but knowing where the helices and probable u-turns were, was critical.

Have you considered pre-smoothing the ED? That might be important for taking advantage of human abilities.

Thanks again for a fun puzzle of real data!

P.S. I was able to do this puzzle. But maybe the puzzle was easy? Can you say if computers were able to fit this ED with no trouble?

brow42's picture
User offline. Last seen 1 week 2 days ago. Offline
Joined: 09/19/2011
Groups: None
smoothing

Maybe smoothing should be a slider! :)

alwen's picture
User offline. Last seen 4 days 7 hours ago. Offline
Joined: 10/03/2011
align to density

I agree with Brow, this one was fun especially once I saw SteveB's screen shot early on and started to get a feel for hauling the denovo into the cloud.

(I've entered a feedback about the Align to Density button, though. Compared to the alignment tool, this button does not align the protein to the density, despite the text on the button.)

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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