puzzle picture
721: Solo Hand-Folding Sepsis Puzzle 3
Status: Closed

Summary

Name: 721: Solo Hand-Folding Sepsis Puzzle 3
Status: Closed
Created: 05/28/2013
Points: 100
Expired: 06/04/2013 - 14:00
Difficulty: Intermediate
Description: We are giving you Museka's solution from Puzzle 684 as a starting model to work on, we have deleted 1 residue (you may delete even more). The sugar molecule bound to this protein is part of a larger carbohydrate structure that is a component of the bacterial cell surface; it is not an isolated sugar as implied by the crystal structure. Therefore, it is crucial that the top portion of the sugar be free of obstructions from the protein; so your designs should only access the sugar from the bottom and sides. More details in the puzzle comments. Because this is a Hand-Folding round, only GUI scripts are allowed and sharing has been disabled.
Categories: Design, Hand-Folding, Overall

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Comments

beta_helix's picture
User offline. Last seen 15 hours 56 min ago. Offline
Joined: 05/09/2008
Groups: None
More info:

Museka's solution from Puzzle 684 was one of our favorite player designs because it only interacts with the sugar from one side and not from the top where there is a large carbohydrate structure (see puzzle description).

We have taken Museka's model, frozen the sheet and deleted one residue from the end of the helix as we'd like that helix to be even lower when it packs against the sugar molecule.

If you'd like to know more about what the Scientists working on this Sepsis protein are looking for, here is a link to the Scientist Chat with Zeckendorff, and here is the Sepsis Blogpost.

If you want to flag a particular solution for us to look at (even if it is not your top-scoring solution) you can use the "Upload for Scientists" button where you can send us up to 3 solutions per puzzle.

___________________________________________

If you are new to Foldit, make sure you have completed Intro Puzzles 7-1 through 7-4 before trying this puzzle.
___________________________________________

This puzzle has the ResidueIE filter on (to try to ensure that PHE, TYR, and TRP residues are scoring properly) and we've increased the Ligand Score to promote interactions with the sugar.

Tip: To see the parts of the sugar that you can bond to, check Show bonds (non-protein) and Show bondable atoms in the View menu. Make sure Show bonds (loop) and Show bonds (sidechain) are also on. Blue can bond to red, and purple can bond to either blue or red.

___________________________________________

This is a Hand-Folding Round:

This round only GUI scripts are allowed and sharing has been disabled. After this puzzle expires, the puzzle will be re-posted and LUA scripts and sharing will be allowed. You'll be able to load in your solutions from this puzzle and use scripting and sharing.

Joined: 09/21/2011
Groups: Void Crushers
Placing the protein

It is a pity that you can place the segments above the sugar and make a good score that way.
It should be a forbidden area.

marie_s's picture
User offline. Last seen 33 weeks 5 days ago. Offline
Joined: 05/18/2008
Groups: None
Ligand bonds score low

This puzzle could have a better reward for bonds with the ligand

beta_helix's picture
User offline. Last seen 15 hours 56 min ago. Offline
Joined: 05/09/2008
Groups: None
Really?

We used the same weights as last time where we had increased the Ligand Score by a factor of 10 to promote interactions with the sugar:
http://fold.it/portal/node/994976#comment-22673

We could try increasing it even more, but it might result in some odd behavior!

bertro's picture
User offline. Last seen 8 weeks 5 days ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
no way to add segments once removed unless reset?

Did I miss something?

There seems to be no way to add segments once removed unless you reset?

beta_helix's picture
User offline. Last seen 15 hours 56 min ago. Offline
Joined: 05/09/2008
Groups: None
Sorry bertro, this is a bug:
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