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831: Abeta Loop Closure B
Status: Closed

Summary

Name: 831: Abeta Loop Closure B
Status: Closed
Created: 01/07/2014
Points: 100
Expired: 01/26/2014 - 23:00
Difficulty: Intermediate
Description: This puzzle builds on a piecewise design solution from Puzzle 808. Build loops to close the cutpoints between secondary structure elements to create an Abeta-binding protein! The two starting structures were derived from a single solution by gitwut and martinzblavy, but have different loop arrangements. Reset the puzzle to cycle through both starting structures. See the puzzle comments for more details. This puzzle will be open for two weeks.
Categories: Design, Overall

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Comments

bkoep's picture
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Joined: 11/15/2012
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More information:

We've tried to estimate the number of residues required to close each loop, but you may prefer to distribute these residues differently. You can delete residues from one loop and reinsert them into another, although you cannot add additional residues to this puzzle.

There is no RMSD filter for this puzzle, but there are some constraints to help keep the secondary structure pieces in place. Note also that you can wiggle the backbone of the Abeta peptide, although there are constraints to keep the two Abeta strands in a sheet.

viosca's picture
User offline. Last seen 1 year 2 weeks ago. Offline
Joined: 10/16/2013
Puzzle Requirements?

In this design puzzle, is it a requirement that all the design residues are used?

Thanks,
Randy

bkoep's picture
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Joined: 11/15/2012
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Not at all

Please feel free to delete residues from this puzzle. In fact, shorter loops are generally more likely to fold up as predicted, however, longer proteins tend to score better in Foldit. If you have a solution you think is a good design but doesn't score as well because it has fewer residues, please share it with us using the Upload for Scientists button!

bkoep's picture
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Joined: 11/15/2012
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Extended deadline

The expiration date for this puzzle has been extended to Sunday, January 26 to accommodate the delayed release of the newchapter update.

Joined: 02/11/2012
Groups: Geekdo
hangup

My PC cannot handle this one. I barely loaded it, when it hangs. Works with all other puzzles, though...

v_mulligan's picture
User offline. Last seen 34 weeks 6 days ago. Offline
Joined: 03/04/2009
Groups: None
Latest client needed

Have you updated to the latest version of the game client, salish99? The programmers had to fix a couple of little bugs in order to get the loop closure puzzles to work properly, so older versions of the game don't work properly with these puzzles.

If that's not the problem, could you leave a report in the "Feedback" section? The game programmers check that regularly, and can address this if it is a bug. Thank you!

ShielaK's picture
User offline. Last seen 5 years 1 week ago. Offline
Joined: 06/13/2014
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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