puzzle picture
1134: 60 Residue Symmetric Dimer Design: Satisfied H-bonds
Status: Closed

Summary

Name: 1134: 60 Residue Symmetric Dimer Design: Satisfied H-bonds
Status: Closed
Created: 09/02/2015
Points: 100
Expired: 09/10/2015 - 23:00
Difficulty: Intermediate
Description: In this puzzle, the bonus for Hbond networks has been doubled, but only Hbond networks that are at least 75% satisfied will be rewarded. We've also amended this puzzle so that the Core Exists filters should be even easier to satisfy. 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 20 hours ago. Offline
Joined: 11/15/2012
Groups: None
Filters

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

HBond Network: Rewards networks comprising at least three hydrogen bonds, with at least one hydrogen bond spanning the dimer interface. In addition, at least 75% of all polar atoms in the network must make hydrogen bonds.

Core Existence: Monomer: Ensures that at least 18 residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 46 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!

Joined: 04/10/2015
Groups: Beta Folders
Suggestion asked in 1131 and considered

Thank you for considering my suggestion at puzzle 1131 and making this puzzle...

Batz's picture
User offline. Last seen 1 day 42 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
"the Core Exists filters should be even easier to satisfy"

Indeed... I got again full bonus even though the monomers did not touch each other

Batz's picture
User offline. Last seen 1 day 42 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
Is this intended?

In one design, I count 18 orange residues when showing the residues for one monomer (giving correctly +160 bonus).
There is no interaction between the two chains, but when I click to show the buried residues in the complex, I count 22 orange residues (44 in total, resulting in -100, which is right when 46 are required). I observed that green residues for the monomer core exist filter turn into orange when switching to the complex core exist filter.

I think that the residues should be considered equally for both filters, right?

bkoep's picture
User offline. Last seen 2 days 20 hours ago. Offline
Joined: 11/15/2012
Groups: None
Yes, this behavior is intended

Very observant, Batz! The criteria for "buriedness" has been relaxed, but only for the complex filter.

We wanted to relax the Core Exists: Complex filter because it seemed to interfere with H-bond networks. But, since we only want H-bond networks at the interface, the core requirements for the monomer are unchanged.

Joined: 10/30/2012
Groups: Beta Folders
monomer filter any chance

monomer filter

any chance that we can get the monomer filter to relax on one of these so we can play with barrels

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

Core Complex seems more than relaxed; it seems to be not doing anything.

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