puzzle picture
1068: 70 Residue Symmetric Dimer Design
Status: Closed

Summary

Name: 1068: 70 Residue Symmetric Dimer Design
Status: Closed
Created: 03/25/2015
Points: 100
Expired: 04/02/2015 - 07:00
Difficulty: Intermediate
Description: This puzzle again uses separate "Core Existence" filters for the monomer unit and the symmetric complex. Click the "Show" checkbox beneath the Core Existence filter to see which residues have been identified as Core (orange), Boundary (green), or Surface (blue). There are several other filters in effect; see the puzzle comments for 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!
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User offline. Last seen 2 days 6 hours ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Monomer: Ensures that at least 19 residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 42 residues are buried in the core of the entire complex (including the interface between monomer units).

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.

Joined: 09/21/2011
Groups: Void Crushers
No penalty fot hydrophobic residues

Havent mutated anything, so I would expect a penalty for having lots of isoleucines on the surface.
To my supprise I have the SS design bonus.
Shared nopenalty with scientists.

bkoep's picture
User offline. Last seen 2 days 6 hours ago. Offline
Joined: 11/15/2012
Groups: None
You're correct

In this puzzle we've omitted the penalty for exposed hydrophobics and buried hydrophilics. I've amended the filter description—thanks for the catch!

Batz's picture
User offline. Last seen 10 hours 21 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
no penalty for Core Existence: Complex

I am getting the bonus for the Core Existence Filter regarding the complex, although the monomers are miles away from each other...

bkoep's picture
User offline. Last seen 2 days 6 hours ago. Offline
Joined: 11/15/2012
Groups: None
Large core?

This can happen if your monomer unit has enough residues in the core (21 in this case) to satisfy both filters. Perhaps this Complex Core Existence filter isn't stringent enough!

Batz's picture
User offline. Last seen 10 hours 21 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
Right

exactly 21 residues in the core of the monomer...

Joined: 09/24/2012
Groups: Go Science
same for me (my current top score)

I suppose you are not interested and it's better to abandon this configuration?

bkoep's picture
User offline. Last seen 2 days 6 hours ago. Offline
Joined: 11/15/2012
Groups: None
Correct

We're only interested in solutions where the two monomers form an interface.

Perhaps the filter threshold is too low, but in this puzzle we wanted to allow players some more room to explore new conformations.

Joined: 06/24/2008
Groups: Void Crushers
Core?

At the moment my best scoring solution has the two parts very very far apart.

spmm's picture
User offline. Last seen 40 weeks 2 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
type of symmetry

Would you please state the type of symmetry being used for each of these puzzles. Thanks

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