puzzle picture
1018: 65 Residue Symmetric Trimer Design (REPOSTED as 1018b)
Status: Closed

Summary

Name: 1018: 65 Residue Symmetric Trimer Design (REPOSTED as 1018b)
Status: Closed
Created: 11/21/2014
Points: 0
Expired: 12/02/2014 - 19:00
Difficulty: Intermediate
Description: It's been a long time since our last Symmetric Design puzzle, and Foldit has seen a lot of improvements in the mean time! This puzzle uses two "Core Existence" filters. One checks that the monomer unit of your design contains a well-packed core, and another ensures that the entire symmetric complex has a buried core. Click the "Show" checkbox beneath the Core Existence filter to see which residues have been identified as Core (orange), Boundary (green), or Surface (blue). 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!
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Comments

bkoep's picture
User offline. Last seen 6 hours 58 min 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: Monomer: Ensures that at least 25% of the residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 30% of the 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!

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

Joined: 12/06/2008
Groups: Contenders
OMG, the lag!

195 mutable segments. Presented without further comment.

Joined: 12/06/2008
Groups: Contenders
Monomer and Complex filters reversed?

I notice that while constructing my monomer, the "complex" filter requirement was met, while the "monomer" requirement still has a thousand-plus point penalty.

How can this be? The three pieces of the complex were light years apart, while my beautiful three sheet, three helix monomer was complete and ready to integrate into the trimer.

Do you have the filter names reversed?

Batz's picture
User offline. Last seen 17 hours 5 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
There must be another thing

There must be another thing gone wrong.
I met the filter for the complex completely, but I think the penalty is just to high for the single monomer, I have 17 orange residues in my monomer, wich means about 26 %, but still -1650 points (while 850 points gained from the starting 2500). Means just 1650 points too much.

Joined: 09/24/2012
Groups: Go Science
I confirm

Yes it seems that the filter names are reversed

Joined: 09/24/2012
Groups: Go Science
No

Sorry, it's not reversed. But is the monomer core filter working well?

Joined: 10/30/2012
Groups: Beta Folders
this is brutal

this is brutal

frood66's picture
User offline. Last seen 2 hours 39 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
same issue...21 segs orange

same issue...21 segs orange in monomer. But a penalty of 1500 from the filter.

As for being 'Brutal', this puzzle needs serious machine power. The recent 90 seg monomer puzzle (filtered) was pushing the limits for many.

spmm's picture
User offline. Last seen 1 year 2 weeks ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
agree about monomer core filter

I can usually get a bonus on the 'core existence' and I am still way off over 1000 points and I have tried 3 different designs.
Getting the core complex is trivial and I'm sure my ultracompact designs shouldn't be getting the complex bonus so easily.
What is worse is that it is so bad there doesn't seem to be much option to do anything interesting which may make more advantage of the trimer.
Also agree that it is painful to work with with especially after 3 tries.
All a bit disappointing.

Batz's picture
User offline. Last seen 17 hours 5 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
Does everyone has this problem?

It seems that some players still have remaining -1600 points and don't get the +160 bonus instead.
But does everyone has this problem?
The best score is about 12700 points but many players are around 10000 to 11000, which makes a difference of about 1000 points still...

Batz's picture
User offline. Last seen 17 hours 5 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
*at least 1000

*at least 1000 points.
Probably even about 2000

spmm's picture
User offline. Last seen 1 year 2 weeks ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
all in the same boat

Probably the top scorers have just got better designs - it will be the same penalty for everyone I guess. Sure takes a lot of the fun out sym puzzles tho :(

Joined: 09/24/2012
Groups: Go Science
a real chalenge (i like it but it takes me more time !!)

It took me hours (because of the machine ressources needed) to test 4 different designs.

On all designed, bizarre enough, the complex core filter gave very quick good points even when the monomers were still completely appart ?! The monomers core penalty always stayed very high.

My best design today (11754 pts, mainly helixes) have still -2050 on Monomer Core design filter (all other filters have bonus). However, it seems to be a good compact monomer.

On another one made from sheets only, I bizarrely have a smaller penalty (around -1700) for monomer design (even if visually, it looks like not compact enough).

On another one, I have sheets and helixes, with a reasonable Core malus but still high negative.

I wonder:

-is it possible that this monomer core filter includes some other hided filters like being obliged to have some minimum number of sheet bonds?

jflat06's picture
User offline. Last seen 2 weeks 2 days ago. Offline
Joined: 09/29/2010
Groups: Window Group
.

This puzzle has been reposted:

http://fold.it/portal/node/1998780

This repost addresses the monomer core exists problem.

You now need only 16 residues in the core of the monomer to pass the filter.

You should be able to load in your solutions from this puzzle into 1018b.

Joined: 09/24/2012
Groups: Go Science
An evaluation

I would be interested to know which monomer core filter score have been achieved by other players for this puzzle. I never reached better than -1000 (in Low wiggle power mode).

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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