2112: Symmetric Tetramer Design with AlphaFold Predictions

Closed since about 4 years ago

Summary

• Created: February 23, 2022
• Expires: March 02, 2022 at 23:00 UTC
• Max points: 100

Description

Design a symmetric protein tetramer, with 4 identical chains of 80 residues each! This puzzle enables AlphaFold predictions for the monomer subunit of your design, so you can upload your solution for AlphaFold using the AlphaFold prediction tool. AlphaFold will predict the structure of your monomer subunit only (i.e. in the unbound state, in the absence of other symmetric copies). If you load this prediction, then Foldit will attempt to align the prediction with your solution. If you continue working off of the AlphaFold prediction, you may need to make adjustments at the interface where the monomer subunit interacts with symmetric copies.



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. 22,301
• 2. Anthropic Dreams 63 pts. 22,202
• 3. Go Science 37 pts. 22,049
• 4. Gargleblasters 21 pts. 21,310
• 5. Void Crushers 11 pts. 21,151
• 6. Beta Folders 5 pts. 21,113
• 7. Australia 2 pts. 17,259
• 8. Marvin's bunch 1 pt. 15,548
• 9. Ogre's lab 1 pt. 0
• 10. incognito group 1 pt. 0

Top soloists

• 21. akaaka 23 pts. 18,906
• 22. Skippysk8s 21 pts. 18,855
• 23. MicElephant 19 pts. 18,829
• 24. WBarme1234 17 pts. 17,941
• 25. dizzywings 16 pts. 17,839
• 26. Anfinsen_slept_here 15 pts. 17,585
• 27. spdenne 13 pts. 17,421
• 28. AlkiP0Ps 12 pts. 17,259
• 29. abiogenesis 11 pts. 17,230
• 30. RWoodcock 10 pts. 17,064

Comments

[bkoep]

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).

Core Existence: Monomer (max +2200)
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 +2400)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 12 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.

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.

Neural Net (max +0)
Achieve an AlphaFold prediction confidence of 80% or more.

[alcor29]

Allowing Glycine causes all mutate functions to load a lot of Glycine in helices and strands. AF might call for manual changes then but is this really OK or desirable?