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634: Electron Density Puzzle 11
Status: Closed


Name: 634: Electron Density Puzzle 11
Status: Closed
Created: 09/13/2012
Points: 100
Expired: 10/04/2012 - 12:00
Difficulty: Intermediate
Description: In this electron density puzzle, we're giving you some more realistic, noisy density. You'll have to use the electron density as a guide in order to find the correct fold. Try to find the best fit for the protein inside of the guide - but remember that since the density is noisy, it isn't always correct. We have posted the secondary structure predictions in the puzzle comments. Get started by completing the electron density intro level (5-3).
Categories: Electron Density, Overall, Prediction

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beta_helix's picture
User offline. Last seen 2 weeks 1 day ago. Offline
Joined: 05/09/2008
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Please use these 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 Valines at residues 13, 31, 52 & 92-93 are highly predicted to be part of a helix. However, the Valine at residue 81 isn't predicted to be anything!

gramps's picture
User offline. Last seen 8 years 11 weeks ago. Offline
Joined: 12/16/2010
new public recipe installs the 634 structure predictions

new public Recipe: 634 comment structs

I've put a detailed description of how I built this recipe into the recipe comments. Yes, marie, I know that needs to go into the wiki too :-)

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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