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485: Quick Alignment Puzzle 482
Status: Closed

Summary

Name: 485: Quick Alignment Puzzle 482
Status: Closed
Created: 11/27/2011
Points: 60
Expired: 12/01/2011 - 03:30
Difficulty: Intermediate
Description: This is a quick repost of Puzzle 482: Advanced Alignment Puzzle, but this time we are providing you with secondary structure predictions that are posted in the puzzle comments and included in the starting structure as well. These predictions are from the SAM-T08 server (as requested in the previous puzzle comments: http://fold.it/portal/node/991105). Check out that page for more hints and make sure you beat Intro Puzzles 6-1 through 6-3 before playing this puzzle.
Categories: Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 1 day 6 hours ago. Offline
Joined: 05/09/2008
Groups: None
Please try to 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 two Valines at residues 84 & 86 are highly predicted to be part of a sheet. However, the Valine at residue 9 is predicted to be either part of a loop or sheet.

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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