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1398: Extra Large Monomer Design: Smaller Core

Closed since over 8 years ago

Intermediate Overall Design

Summary

Created
June 30, 2017
Expires
Max points
100
Description

This puzzle challenges players to design a single-chain protein with 95-120 residues. The Core Existence filter has been relaxed such that only 25% of residues need to be buried in the protein core. The starting structure has 95 residues, but more can be added at a cost of 23 points per residue. 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!

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Comments

bkoep Staff Lv 1

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

Core Existence: Ensures that at least 25% 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 residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 95. Players may use up to 120 residues in total.

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

Skippysk8s Lv 1

I had hoped this larger protein would allow a Rossmann 2 by 2 fold. It did not ever get to ideal loops with either 6 segment sheets, as in the Koga & Koga paper or 8 segment sheets. I have submitted both to scientists. I think it proves our "ideal loop" library is too small