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 Gargleblasters
    1. Gargleblasters
    100 pts. 10,904
  2. Avatar for Beta Folders 2. Beta Folders 63 pts. 10,858
  3. Avatar for Go Science 3. Go Science 37 pts. 10,701
  4. Avatar for Anthropic Dreams 4. Anthropic Dreams 21 pts. 10,580
  5. Avatar for Contenders 5. Contenders 11 pts. 10,565
  6. Avatar for Void Crushers 6. Void Crushers 5 pts. 10,459
  7. Avatar for L'Alliance Francophone 7. L'Alliance Francophone 2 pts. 10,272
  8. Avatar for Trinity Biology 8. Trinity Biology 1 pt. 7,051
  9. Avatar for Marvin's bunch 9. Marvin's bunch 1 pt. 6,695
  10. Avatar for freefolder 10. freefolder 1 pt. 772
  1. Avatar for dcrwheeler 11. dcrwheeler Lv 1 66 pts. 10,563
  2. Avatar for caglar 12. caglar Lv 1 63 pts. 10,523
  3. Avatar for phi16 13. phi16 Lv 1 60 pts. 10,506
  4. Avatar for Timo van der Laan 14. Timo van der Laan Lv 1 58 pts. 10,459
  5. Avatar for fiendish_ghoul 15. fiendish_ghoul Lv 1 55 pts. 10,417
  6. Avatar for isaksson 16. isaksson Lv 1 53 pts. 10,401
  7. Avatar for retiredmichael 17. retiredmichael Lv 1 50 pts. 10,399
  8. Avatar for Skippysk8s 18. Skippysk8s Lv 1 48 pts. 10,367
  9. Avatar for pvc78 19. pvc78 Lv 1 46 pts. 10,300
  10. Avatar for toshiue 20. toshiue Lv 1 44 pts. 10,285

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.