puzzle picture
1196: 70 Residue Monomer Design: More Sheets!
Status: Closed

Summary

Name: 1196: 70 Residue Monomer Design: More Sheets!
Status: Closed
Created: 02/19/2016
Points: 100
Expired: 02/25/2016 - 23:00
Difficulty: Intermediate
Description: This is a basic 70 residue design puzzle without any Fragment Filter. See the puzzle comments for filter 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

Top Groups

RankGroupScorePoints
1Void Crushers10,333100
2Anthropic Dreams10,30177
3Contenders10,28058
4Beta Folders10,25143
5L'Alliance Francophone10,22931

Top Evolvers

Top Soloists



Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 2 days 12 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: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that at least 50% of residues are in sheets; penalties are incurred if fewer than 50% of residues form sheets.

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

smilingone's picture
User offline. Last seen 7 hours 17 min ago. Offline
Joined: 09/19/2011
Groups: Beta Folders
should this be 1196 since I don't see 1196 posted

Just curious...

alcor29's picture
User offline. Last seen 10 hours 20 min ago. Offline
Joined: 11/16/2012
Why does it say "More

Why does it say "More Sheets!" when it is an open design?

LociOiling's picture
User offline. Last seen 7 hours 4 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
secondary structure filter

The secondary structure filter is what enforces more sheets:

Secondary Structure: Checks that at least 50% of residues are in sheets; penalties are incurred if fewer than 50% of residues form sheets.

alcor29's picture
User offline. Last seen 10 hours 20 min ago. Offline
Joined: 11/16/2012
Thanks. I've got to read

Thanks. I've got to read things more carefully.

dbuske's picture
User offline. Last seen 14 hours 28 min ago. Offline
Joined: 09/22/2011
Groups: Beta Folders
Sheets Filter not working?

I had way more then 50% residues in sheets and it still said there was not enough.

bkoep's picture
User offline. Last seen 2 days 12 hours ago. Offline
Joined: 11/15/2012
Groups: None
Correct hydrogen bonds?

Are your sheets forming hydrogen bond "ladders" correctly?

The Secondary Structure Filter detects helices and sheets by their hydrogen bonding patterns. Simply assigning a region of your protein as "Helix" or "Loop" (e.g. using Structure Mode in Original Interface) will not affect the filter. Likewise, a single beta strand will not be counted by the filter unless it makes proper hydrogen bonds with a neighboring beta strand.

LociOiling's picture
User offline. Last seen 7 hours 4 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
more fun with filters

I just noticed some odd behavior from the secondary structure and secondary structure design filters.

On one design, segment 11 is flagged by the SS Design filter. The segment is glycine, but it's intended to be a loop between two sheets. It does show a bond to segment 13, which is marked as a sheet, but I'm surprised the filter has decided it's part of a sheet.

Mutating segment 11 also has odd effects. Mutating to proline fixes 3 invalid residues in the SS Design filter, but changes the Secondary Structure filter from +500 to -300. (All I did was select segment 11 in the selection interface, then m -> p.)

Mutating segment 11 to threonine kept the secondary structure filter at +500, and fixed one invalid residue for the SS Design filter, which is what I would expect.

It seems the Secondary Structure and SS Design filters have a bit of a "hair trigger" on puzzle 1193, but perhaps it's just me. I've shared the solution in question with the scientists.

Here are the screenshots:

1196: glycine at segment 111196: glycine at segment 11

1196: proline at segment 111196: proline at segment 11

1196: threonine at segment 111196: threonine at segment 11

Susume's picture
User offline. Last seen 4 hours 36 min ago. Offline
Joined: 10/02/2011
All about the bonds

Proline is unable to form a sheet bond, so putting it in a place that had a sheet bond will cause the sheet bond to disappear, even though the backbone position does not change. This loss of a bond was enough to reclassify both the proline and the residue it was previously bonded to from "sheet" to "not sheet." This would make the aas in those positions allowable under SS design, but lower your count of sheets. Putting the threonine in made the sheet bond reappear, changing both those residues back to sheet. Not sure why the glycine on the right in your pictures was reclassified though, given that its bonding apparently did not change.

brow42's picture
User offline. Last seen 1 day 19 hours ago. Offline
Joined: 09/19/2011
Groups: None
sandwiches vs barrels

A lot of people will be doing sandwiches, and a lot of people will be doing beta barrels. What structural feature causes a sheet to prefer one over the other?

Joined: 07/21/2013
Groups: Beta Folders
1196 evolving rank

the 1196 puzzle page shows brgreening with a rank of 16 and a score of 10224.120

the Foldit DevPrev app shows me with a rank of 23 and a score of 10224.120 in the box at the top center of the screen

the Evolver Competition on the right side of the screen shows me with an evolver rank of 7

I have Conditions Satisfied of 2 out of 2 and it looks like a valid evolver solution.

Anyone else seeing these evolver rank anomalies?

Get Started: Download
  Windows    OSX    Linux  
Windows
(Vista/7/8)
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, Microsoft, Adobe, RosettaCommons