puzzle picture
682: 40 Residue Symmetric Trimer
Status: Closed


Name: 682: 40 Residue Symmetric Trimer
Status: Closed
Created: 03/01/2013
Points: 100
Expired: 03/14/2013 - 15:00
Difficulty: Intermediate
Description: We are giving you a symmetric trimer of 40 residues to design. Remember, a symmetric protein relies not only on how well folded each part is, but also on how well they interface together - and a symmetric trimer can be thought of as having three 2-fold interfaces. There are multiple filters enabled on this puzzle that should lead you in the right direction. The ResidueIE filter ensures PHY, TYR, and TRP residues are scoring well. The "Core Exists" filter ensures the number of residues in the core is between 30% and 70%. The "Polar Core" filter that the residues in the core are properly hydrophobic. The "Layer Design" filter looks at the interactions of the residues based on the surface area of the protein. Residues can be either in the core, on the boundary or on the surface of the protein. Depending on the surroundings, the "Layer Design" filter will give you a bonus if your amino acid matches what it was expecting. Press TAB on each residue to find out more about these filters.
Categories: Design, Overall, Symmetry

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Joined: 12/06/2008
Groups: Contenders
Alanine is polar??

I think we have a bug, here. I have the "too many polar residues in the core" penalty. Every one of the highlighted sidechains is an alanine.

Correct me if I'm wrong, since it's been almost thirty years since I studied protein chemistry... but isn't alanine one of the more hydrophobic sidechains?

tamirh's picture
User offline. Last seen 7 years 18 weeks ago. Offline
Joined: 05/11/2012
Looking into this

Hey Boots,

We haven't been able to reproduce this issue. If you still have it, could you share a solution where this is happening with yourself and then let us know the title of the save? Thanks.

Joined: 12/06/2008
Groups: Contenders

Sorry... but I restarted the puzzle and exceeded the score of the version that had a half dozen alanines, all marked as too polar for the core. I did not make any manual saves.

But I have a bigger issue with this puzzle. I will outline it, below.

Joined: 03/02/2013
Groups: None
how do you click start

how do you click start

Joined: 06/24/2008
Groups: Void Crushers

Boots is cheating!! He has studied protein chemistry!! I thought only players that believed it was all magic could play!

Joined: 06/24/2008
Groups: Void Crushers

682 is exhibiting the shutter wiggle in the new devprev

Joined: 12/06/2008
Groups: Contenders

Wiggle doesn't happen unless you continuously start and stop the wiggle function. And even then, very soon it just stops wiggling, altogether.

Also: mutate has slowed to a crawl. It's impossible to tell if mutate has mutated all it can, or if I'm expected to wait an additional hour to see if anything actually happened.

In fact, everything on this puzzle works in slow-motion. Un-fun, practically unplayable. And no. I have a kick-butt computer, so it's not a memory or CPU issue.

Joined: 03/06/2013
Groups: None

how do you find a game what ever and play

Joined: 12/06/2008
Groups: Contenders
The big ol' helix wins... again.

Once again, a single, huge helix ends up with a much higher score than any other structure.

I designed this thing with four helices, separated by loops. Top score = 11607. Re-designed it with three helices, separated by loops. Best score = 11854.

Just for grins, I made on long, 40-residue helix with no bends in it at all. A huge cylinder. It's scored 12239, almost four hundred points above the best of my other structures.

The mega-helix loses about 200 points for an inadequate core. My multi-helix structures both get 60 bonus points for a good core.

The mega helix gets 150 bonus points for no invalid sidechains, while my multi-helix structures lose 10 or 20 points for 2 or 3 invalid sidechains.

How is it possible that a structure that violates the core requirements and could never exist in real life possibly score hundreds of points over structures that could exist?

tamirh's picture
User offline. Last seen 7 years 18 weeks ago. Offline
Joined: 05/11/2012
Rosetta holes

That's unfortunately an issue with how Rosetta weights helices. We are attempting to get around this score hole and these filters were supposed to help with that. We will analyse all of the solutions and determine if we need new filters, changes to the weights of the filters, or if we need to make changes elsewhere.

Thanks for all the hard work Boots and everyone else.

Joined: 03/08/2013
"Not enough residues in core"

I have no idea how to make it stop. I cannot add any sidechains to the core, because on this level, you cannot add segments!!

Joined: 12/06/2008
Groups: Contenders
You need to....

You need to bend the thing so that parts of it are near other parts of it, ultimately having several pieces of the backbone and their sidechains in the center of the structure. A single helix or sheet won't cut it. You'll need at least two structures, preferably three or more.

brow42's picture
User offline. Last seen 23 weeks 2 days ago. Offline
Joined: 09/19/2011
Groups: None
I saw similar things

I started this late. I see the same things as Boots. When I played it, I saw:

The very first mutate of the puzzle took at least 30 seconds to change anything (they were all alanine). Subsequent mutates were normal.

It complained about alanine in the core, so I changed those to valine (unfortunately this unpacked my protein and I got core existence penalty). Also it complained about a histadine on an external sheet surface.

Wiggle at CI 1.0 is normal, but < 1.0 it stutters. It's about the same as the last puzzle, post fix.

tamirh's picture
User offline. Last seen 7 years 18 weeks ago. Offline
Joined: 05/11/2012
Note to devprev users

There was an issue where you could have invalid high scores uploaded to the server. The fix for this has just been pushed out to devprev.

What we are doing with the puzzle is we will re-score the solutions once the puzzle closes and update any scores that happen to be posted without filters enabled. To prevent your score from changing, try and make sure your highest scoring solution has filters enabled after updating to the new devprev.

We realize this may not be possible in some cases, so if you can't reach your current invalid score with a valid score let us know so we will know which solution of yours to re-score.

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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