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1647: Symmetric Dimer Design: 100 Residues

Closed since almost 7 years ago

Intermediate Overall Design Symmetry

Summary

Created
March 11, 2019
Expires
Max points
100
Description

This symmetric design puzzle has C2 symmetry, with two symmetric chains. There is no H-bond Network Objective in this puzzle, so the interface can be completely nonpolar (orange sidechains). No more than 50% of residues may form helices, and all loops must match one of the Ideal Loop Building Blocks found in the Blueprint tool. See the puzzle comments for Objective 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!

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Comments

bkoep Staff Lv 1

Core Existence: Monomer (max +3000)
Ensures that at least 30 residues are buried in the core of the monomer unit.

Core Existence: Complex (max +3700)
Ensures that at least 74 residues are buried in the core of the entire complex (including the interface between monomer units).

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

stomjoh Lv 1

If you want exactly 74 residues in the complex core, just say so. Anything under 74 is a point reduction - got it.
But you're also penalizing points for having more than 74 residues in the complex core???

bkoep Staff Lv 1

Whoa, that's not right. None of these objectives should penalize you for having too many core residues. Can you share your solution with scientists?

Also, are there any details about the Objective penalty (if you hover your cursor over the Objective description)?

actiasluna Lv 1

If I can replicate I'll share. I had fixed a bad loop and when it wiggled out too many residues in the core penalty came up. I noticed that penalty last night too when I was folding the pattern.
Shared solution. Hover says "Too many residues in the core. Move core (orange) residues out to the surface (4 to go)"

It appears to penalize 20 points per "extra" residue.