puzzle picture
1569: Design Partition Tournament: Phase One
Status: Closed

Summary

Name: 1569: Design Partition Tournament: Phase One
Status: Closed
Created: 08/30/2018
Points: 100
Expired: 09/13/2018 - 23:00
Difficulty: Intermediate
Description: This the Phase One design puzzle for the Protein Design Partition Tournament! Players have two weeks to craft their best protein design, which will have to defend itself in Phase Two of the tournament. For players who do not wish to participate in the tournament, this puzzle will also behave like a normal Foldit puzzle, and points will be awarded to top-ranking players and teams as usual. Players may use 70-100 residues, at a cost of 32 points per residue; and designs with more than 10% helices will be penalized 10 points per extra residue in a helix.

To submit a design for the tournament, players must save their chosen solution with the title "Tournament Submission" and share the solution with scientists using the Upload for Scientists button in the Save Solution menu. Only soloist solutions will be accepted as tournament submissions. See the blog for tournament details.
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 14 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Residue Count: Normalizes for extra residues inserted beyond the starting 70, at a cost of 32 points per residue. Players may use up to 100 residues in total.

Secondary Structure: Only 10% of residues may form helices. Additional helices will incur a penalty of 10 points per residue.

jeff101's picture
User offline. Last seen 17 hours 43 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
No usual restrictions?

In Puzzle 1566: Small Monomer Design,
we had the Objectives below:

Interaction Energy: Monitors that all
PHE, TYR, and TRP residues are scoring well.

SS Design: Prohibits all CYS residues.
Prohibits GLY, ALA residues in sheets.
Prohibits GLY, ALA, SER, THR in helices.

Does 1569 have any of these restrictions?
Do you want 1569 to allow disulfide bonds,
for example?

Thanks!
Jeff

bkoep's picture
User offline. Last seen 14 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
No usual restrictions

That's correct; there is no Interaction Energy or SS Design objective in this puzzle.

However, CYS residues have been disabled in this puzzle, so players should not be able to design disulfide bonds.

frood66's picture
User offline. Last seen 2 hours 53 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
cysteine - bridges

bit odd that players were not told this at the start - don't u think?

Susume's picture
User offline. Last seen 15 hours 50 min ago. Offline
Joined: 10/02/2011
Too many aromatics

Mutate is putting in too many tyrosines, and in the absence of a filter, the script I am running is keeping them.

jeff101's picture
User offline. Last seen 17 hours 43 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
More aromatics like tyrosine may be a good thing

To make sure your solutions have sequences that can't easily be
rebuilt as helices, it may help to include tryptophan, tyrosine,
phenylalanine, isoleucine, valine, and threonine residues that
https://en.wikipedia.org/wiki/Protein_secondary_structure
says prefer to adopt β-strand conformations. It may also help
to include glycine and proline (helix-breaker) residues and to
avoid the helix-favoring MALEK (methionine, alanine, leucine,
glutamate, and lysine) residues. Another idea is to use
sequences that alternate between hydrophilic and hydrophobic
residues, as often occurs in sheets, rather than other patterns
that often occur in helices.

Joined: 06/24/2008
Groups: Void Crushers
tournament puzzle

can we submit more than one?

bkoep's picture
User offline. Last seen 14 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
One submission allowed

Each player may submit only one design for the tournament. If a player submits multiple solutions with the title "Tournament Submission", then only the most recent submission will be considered for Phase Two of the tournament. The reason for this is to make sure everyone has an equal chance in the Phase Two selections.

However, we still want to see your designs! If you develop several designs that you like, please share them all with us using the Upload for Scientist button! Even though we will only consider one submission for the tournament, we will still run our regular analysis on all designs from this puzzle. We always look at the scientist-shares in design puzzles, and it's especially helpful if you can save them with an informative title and description!

Joined: 06/24/2008
Groups: Void Crushers
Humm

OK, I wondered because if you wiggle the preferred solution on Medium you may not be able to do much with it the second round.

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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