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1263: 70 Residue Monomer Design: Ideal Loop Filter
Status: Closed

Summary

Name: 1263: 70 Residue Monomer Design: Ideal Loop Filter
Status: Closed
Created: 07/20/2016
Points: 100
Expired: 07/29/2016 - 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 2 days 2 hours 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 70 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."

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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, Microsoft, Adobe, RosettaCommons