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1433: Medium Monomer Design

Closed since almost 5 years ago

Intermediate Overall Design


September 22, 2017
Max points

This puzzle challenges players to design a single-chain protein with 75-90 residues. We've softened the penalties associated with the Core Existence filter, which have typically been very steep. The starting structure has 75 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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bkoep Staff Lv 1

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 residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 75. Players may use up to 90 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."

Susume Lv 1

You might consider reducing the per-residue penalty a little bit since the core bonus is less. 23 has always been quite steep (that appears to be the regression coefficient only for the top 10 solutions on fixed-length puzzles, so that any solution worse than top 10 quality loses more than it can regain when adding residues). Now with a smaller overall filter bonus, the average points per residue are also reduced.

SanDeGoSi Lv 1

Приветики мальчики и девочки. А как интересно Вы
проводите своё свободное время?

SanDeGoSi Lv 1

Приветики мальчики и девочки. А как интересно Вы
проводите своё свободное время?