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662: Blind Electron Density 4
Status: Closed


Name: 662: Blind Electron Density 4
Status: Closed
Created: 12/20/2012
Points: 100
Expired: 01/05/2013 - 08:00
Difficulty: Advanced
Description: This is our fourth electron density puzzle with real data. Like our previous puzzles, we were able to pinpoint which regions belong to a single copy, though the density itself is less clear. Try to fit the protein into the density to get the best score! Secondary Structure Predictions are posted in the puzzle comments.
Categories: Electron Density, Overall, Prediction

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beta_helix's picture
User offline. Last seen 5 hours 17 min ago. Offline
Joined: 05/09/2008
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Secondary structure predictions:

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 amino acid Leucine at residue 37 is highly predicted to be part of a sheet. However, the Valines at residues 6-7 & 97 have an equal probability of being anything.

bertro's picture
User offline. Last seen 17 weeks 2 days ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Smoother and Cleaner Density Cloud possible?

I believe it is possible to improve this density cloud clarity:

1) The current density map seems to have been saved with a step of 2 (judging by the rough angles of the blobs) giving us a much rougher image to work with than with a step of 1.

2) Plus some dust cleaning (removing small blobs) would also greatly enhance our ability to navigate and distinguish the shape of the protein.

Please, could you re-submit the puzzle with a smoother/cleaner density cloud?


grogar7's picture
User offline. Last seen 2 days 13 hours ago. Offline
Joined: 10/03/2011
Puzzle disappeared?

This puzzle seems to have disappeared from my list of available science puzzles. It is not supposed to have expired for several hours. Explanation?

tamirh's picture
User offline. Last seen 8 years 25 weeks ago. Offline
Joined: 05/11/2012
we're looking into it.

we're looking into it.

tamirh's picture
User offline. Last seen 8 years 25 weeks ago. Offline
Joined: 05/11/2012
Back up

The puzzle should be back up, Seth took care of it. Thanks for letting us know.

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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, Boehringer Ingelheim, RosettaCommons