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1260: 85 Residue Monomer Design: Ideal Loop Filter
Status: Closed

Summary

Name: 1260: 85 Residue Monomer Design: Ideal Loop Filter
Status: Closed
Created: 07/15/2016
Points: 100
Expired: 07/23/2016 - 23:00
Difficulty: Intermediate
Description: NOTE: The expiration date for this puzzle has been extended by 24 hours, due to some planned downtime close to the puzzle's original expiration date.

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 4 hours 4 min ago. Offline
Joined: 11/15/2012
Groups: None
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 85 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."

tokens's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 11/28/2011
Helix-helix loop

I have a blue-blue-blue helix to helix loop, which is accepted by the ideal loop filter. In fact I made it by defining 3 segments as sheet and running ideal SS on the segments. But this color pattern is not in the list of ideal helix-helix loops shown in the Rama map.

Is this pattern missing in the list of of ideal loops or is it a mistake by the ideal loop filter?

bkoep's picture
User offline. Last seen 4 hours 4 min ago. Offline
Joined: 11/15/2012
Groups: None
Missing from Rama Map

That particular helix-helix loop (and a couple others) is not shown in the Rama Map, but it is fairly common and should be accepted by the filter! Sorry for the inconsistency!

tokens's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 11/28/2011
Thanks for the quick answer.

Thanks for the quick answer.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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