2021: Symmetric Trimer Design: H-bond Networks

Closed since over 4 years ago

Summary

• Created: July 22, 2021
• Expires: July 28, 2021 at 23:00 UTC
• Max points: 100

Description

Design a symmetric protein trimer, with 3 identical chains of 80 residues each! This puzzle includes a Secondary Structure Objective, so no more than 50% of your design can form helices. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.

Top groups

• 1. Contenders 100 pts. 22,224
• 2. Anthropic Dreams 71 pts. 21,912
• 3. Go Science 49 pts. 21,858
• 4. Gargleblasters 33 pts. 21,698
• 5. Marvin's bunch 22 pts. 21,088
• 6. Beta Folders 14 pts. 19,994
• 7. Void Crushers 8 pts. 19,826
• 8. L'Alliance Francophone 5 pts. 19,446
• 9. Australia 3 pts. 18,108
• 10. SETI.Germany 2 pts. 12,727

Top soloists

• 41. Altercomp 8 pts. 17,595
• 42. fishercat 7 pts. 17,545
• 43. xythus 7 pts. 17,429
• 44. Trajan464 6 pts. 17,410
• 45. Skippysk8s 6 pts. 17,379
• 46. abiogenesis 5 pts. 17,148
• 47. Hellcat6 5 pts. 17,058
• 48. tracybutt 4 pts. 16,873
• 49. Beany 4 pts. 16,524
• 50. Todd6485577 4 pts. 16,274

Comments

[bkoep]

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).

Core Existence: Monomer (max +1600)
Ensures that at least 22 residues are buried in the core of the monomer unit.

Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.

H-bond Network (max +1800)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 9 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

[spvincent]

Now there's a new version of Rosetta, perhaps you could allow insertion/deletion of residues again in this type of puzzle.

[bkoep]

The Foldit code will still require some modification before we can allow residue insertions/deletions in symmetry puzzles.

But we appreciate the continued feedback! We read you loud and clear that this is an important feature to add.

[grogar7]

Thanks to the team for recent efforts in improving the code! I have not experienced any crashes on this puzzle, even with the notorious Remix scripts :-)