Placeholder image of a protein
Icon representing a puzzle

1485: Extra Large Monomer Design

Closed since about 8 years ago

Intermediate Overall Design

Summary

Created
February 16, 2018
Expires
Max points
100
Description

This puzzle challenges players to design a single-chain protein with 90-125 residues. The starting structure has 90 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!

Top groups

  1. Avatar for Penn State Biomolecular Engineers 11. Penn State Biomolecular Engineers 1 pt. 0
  2. Avatar for UBCO-BIOC402-2018WT2 12. UBCO-BIOC402-2018WT2 1 pt. 0
  1. Avatar for Enzyme
    1. Enzyme Lv 1
    100 pts. 10,899
  2. Avatar for LociOiling 2. LociOiling Lv 1 97 pts. 10,855
  3. Avatar for actiasluna 3. actiasluna Lv 1 93 pts. 10,823
  4. Avatar for Blipperman 4. Blipperman Lv 1 89 pts. 10,708
  5. Avatar for ZeroLeak7 5. ZeroLeak7 Lv 1 85 pts. 10,697
  6. Avatar for johnmitch 6. johnmitch Lv 1 82 pts. 10,647
  7. Avatar for Bruno Kestemont 7. Bruno Kestemont Lv 1 78 pts. 10,595
  8. Avatar for Galaxie 8. Galaxie Lv 1 75 pts. 10,580
  9. Avatar for Glen B 9. Glen B Lv 1 72 pts. 10,573
  10. Avatar for Bletchley Park 10. Bletchley Park Lv 1 69 pts. 10,565

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 35% 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 90. Players may use up to 125 120 residues in total.

LociOiling Lv 1

The comments say 90 to 125 segments, but I can't add beyond segment 120. That's actually the normal maximum for an "extra large monomer", so we'll assume the 125 was a typo.

bkoep Staff Lv 1

You're correct, that was a typo. Thanks for pointing it out! I've amended the comment.

SaraL Lv 1

I was able to get my protein up to 9826, however after that point the system appeared to 'break'.

Any manner of wiggling other than local would force the protein to come apart and fold to a worse score with negative penalties for loops not scoring high enough and not enough residues in the core.

I tried low/medium power, with clashing importance adjusted from 0.03 to 1.00 - Same result every time.

bkoep Staff Lv 1

That's weird. Can you share your solution using the Share with Scientists button, and we'll take a look?

Susume Lv 1

When a monomer design starts pulling radically out of shape, sometimes it means the "ideal loop" constraints have moved to the wrong spot on the protein due to deleting/adding segments. Open blueprint, and if there are white rectangles on the sequence of letters, drag the rectangles off. That removes the constraints and lets your protein wiggle more freely.