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1251: 90 Residue Monomer Design: Ideal Loop Filter
Status: Closed

Summary

Name: 1251: 90 Residue Monomer Design: Ideal Loop Filter
Status: Closed
Created: 06/24/2016
Points: 100
Expired: 07/01/2016 - 23:00
Difficulty: Intermediate
Description: This puzzle features the new Ideal Loops Filter. The Ideal Loops Filter is meant to encourage the use of the Ideal Loops that are displayed in the Rama Map. It works similarly to the Fragment Filter (but much faster), and will yield a penalty when it detects a loop that does not conform to the ABEGO patterns in the Rama Map. The filter is meant to scan only loops, and will ignore any detected helices and sheets; use the Auto Structures tool to see which regions are considered "loops." See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 7 hours 22 min ago. Offline
Joined: 11/15/2012
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Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.

Residue Count: Penalizes extra residues inserted beyond the 90 residue limit. Players may insert up to 10 extra residues.

Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."

bertro's picture
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Joined: 05/02/2011
Groups: Beta Folders
Quote: "The filter is meant

Quote:
"The filter is meant to scan only loops, and will ignore any detected helices and sheets; use the Auto Structures tool to see which regions are considered "loops." "
End quote.

Comment: The filter often show a bad loop segment that the Auto Structures tool has designated as part of a sheet or helix.

Is this normal?

bkoep's picture
User offline. Last seen 7 hours 22 min ago. Offline
Joined: 11/15/2012
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Maybe

Are all of the highlighted segments part of a sheet or helix? This shouldn't happen, and it would be helpful if you can share this solution with us.

Sometimes, at the edge of a bad loop, the Ideal Loop filter will also highlight one residue of the neighboring helix or sheet. This is just a quirk in the way we're highlighting residues, but it should not affect the filter penalty. The penalty from the Ideal Loop filter does not depend on loop length, e.g. a bad 6-residue loop receives the same penalty as a bad 5-residue loop.

frood66's picture
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Joined: 09/20/2011
Groups: Gargleblasters
yes - but is it intended?

yes - but is it intended?

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