2061: Symmetric Trimer Design with AlphaFold Predictions

Closed since over 4 years ago

Summary

• Created: October 23, 2021
• Expires: October 29, 2021 at 23:00 UTC
• Max points: 100

Description

Design a symmetric protein trimer, with 3 identical chains that assemble together! 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. Go Science 100 pts. 20,546
• 2. Gargleblasters 68 pts. 20,360
• 3. Anthropic Dreams 44 pts. 20,240
• 4. Contenders 27 pts. 20,227
• 5. Beta Folders 16 pts. 20,148
• 6. L'Alliance Francophone 9 pts. 17,784
• 7. BOINC@Poland 5 pts. 17,485
• 8. Australia 3 pts. 17,022
• 9. AlphaFold 1 pt. 15,475
• 10. :) 1 pt. 14,146

Top soloists

• 1. Bruno Kestemont 100 pts. 20,546
• 2. sgeldhof 94 pts. 20,471
• 3. dcrwheeler 88 pts. 20,406
• 4. HuubR 83 pts. 20,358
• 5. silent gene 78 pts. 20,315
• 6. LociOiling 73 pts. 20,148
• 7. grogar7 68 pts. 20,034
• 8. spvincent 63 pts. 20,019
• 9. Galaxie 59 pts. 19,726
• 10. BootsMcGraw 55 pts. 19,678

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 +2000)
Ensures that at least 20 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 3 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.

[jeff101]

I am curious how many residues there are per monomer in this puzzle.

[LociOiling]

They should really include this info in the puzzle description, but there are a couple of easy ways to get it.

In the selection interface, control + a to select all shows the count in the upper left if the GUI is visible.

Otherwise, recipes that include AddMax, AA Edit, print protein, and others give the count.

[jeff101]

I just like to know before I start a puzzle what it entails.