puzzle picture
1109: 80 Residue Symmetric Dimer Design: HBNet
Status: Closed

Soloists



Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 58 min 13 sec 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.

Core Existence: Monomer: Ensures that at least 24 residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 54 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!

bkoep's picture
User offline. Last seen 58 min 13 sec ago. Offline
Joined: 11/15/2012
Groups: None
Inconsistent scoring

Some players have reported a scoring anomaly in similar puzzles; we think this problem will be less pronounced here, but please share with us if you encounter scoring problems when loading a solution!

Joined: 06/24/2008
Groups: Void Crushers
Helices or Not??

Question about 1109. All out H-Bond puzzles have been helices should this be all helices?

bkoep's picture
User offline. Last seen 58 min 13 sec ago. Offline
Joined: 11/15/2012
Groups: None
Anything and everything!

All-helical designs are just fine in this puzzle.

Yet, as always, we encourage players to experiment and try new things! We always take a close look at designs that players Share with Scientists, and here we are especially excited to see what players can do with hydrogen bond networks!

Joined: 07/05/2015
Groups: None
Need help

I can't find out how to play the fold it game.

Susume's picture
User offline. Last seen 1 day 21 hours ago. Offline
Joined: 10/02/2011
HB nets vs. complex core filter

Some on my team are finding that HB nets in the interface push the monomers apart a little (compared with all hydrophobes in the interface) and this causes the loss of the complex core filter points. Because the complex core filter is so discontinuous (huge gain or loss of points all at once) and the HB net points are gained or lost a few at a time, it is hard or impossible to trade out just a few hydrophobes for polars and keep one's score up.

Do natural dimers have a mix of hydrophobes and polars in the interface? If so, maybe an adjustment to the complex core filter is needed. If not, such a mix may not be feasible.

bkoep's picture
User offline. Last seen 58 min 13 sec ago. Offline
Joined: 11/15/2012
Groups: None
Thanks for the feedback!

Yes, natural interfaces tend to have a mixture of hydrophobic and polar interactions.

To be clear, polar residues do contribute to the Core Existence filter. Though, I can see how H-bonding polar residues might have a tendency to push subunits apart from one another to open up the interface—especially if you're simply trying to modify a pre-formed, all-hydrophobic interface. We will consider adjusting the Complex Core Existence filter for future puzzles, thanks for the feedback!

Susume's picture
User offline. Last seen 1 day 21 hours ago. Offline
Joined: 10/02/2011
Voids

If you keep hydrophobes in the middle of the interface and make HB nets around the edges, the nets still force the monomers apart a bit, causing voids to form in the interface.

AryehK's picture
User offline. Last seen 3 years 6 weeks ago. Offline
Joined: 12/11/2014
Groups: Go Science
Re: need help

I reccomend Foldit Wiki for foldit advice
foldit.wikia.com/wiki/Foldit_Wiki

Get Started: Download
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.7 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Search
Only search fold.it
Recommend Foldit
User login
Soloists
Evolvers
Groups
Topics
Top New Users
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons