puzzle picture
1920: MERS-CoV Binder Design: Round 5
Status: Closed


2Go Science23,8630
3L'Alliance Francophone21,7860
5Marvin's bunch20,8500
8Beta Folders20,4340
9Void Crushers20,3670
10Anthropic Dreams20,3500
11Hold My Beer17,6920
12Team Poland16,7200
13Team China13,4210
14Italiani Al Lavoro10,5600
15Foldit Staff00
16Window Group00

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bkoep's picture
User offline. Last seen 6 hours 25 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Buried Unsats (max +500)
Penalizes 60 points for each polar atom that cannot make any hydrogen bonds.

Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 161, at a cost of 55 points per residue. Players may use up to 166 residues in total.

Core Existence (max +1500)
Ensures that at least 25 percent of residues are buried in the core of the monomer unit.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

SS Design (max +500)
Disabled use of CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

DDG Metric (max +1000)
The predicted binding energy of your design. The goal DDG is -40.0 or less.

Contact Surface Metric (max ???)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 400 or more.

Joined: 01/01/2016
Groups: Gargleblasters

I don't know whether it's just me but I've hung three times on this puzzle this morning. Once after an accidental double click, once during a simple shake and once during a mutate.

Joined: 01/01/2016
Groups: Gargleblasters
OK I'm giving up on this

OK I'm giving up on this puzzle. Thought I'd give it another chance but another hang almost immediately while trying to run 'Quickfix'.

g_b's picture
User offline. Last seen 15 hours 22 min ago. Offline
Joined: 04/28/2010
Groups: None
hanging for me also

two times in about 30 minutes - puzzle or new client update?

Joined: 09/29/2016
Groups: Gargleblasters
CSM Bonus?

Hey bkoep, your description of the Contact Surface Metric indicates a Max of +1000; however, in all of the puzzles with CS active, at a value of 400 it's actually been giving +5000 (due to the fact it's a Logarithmic/Scaling bonus instead of Linear).

Is that an oops on the description, or an oops on the Filter?

bkoep's picture
User offline. Last seen 6 hours 25 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Filter error

Hmm, that was an oversight in the Objective setup; we had intended for Contact Surface bonus to cap at +1000. That's a little unfortunate, but I think we will still get useful data from the puzzle, so we won't close it early.

Joined: 09/29/2016
Groups: Gargleblasters
Alright, thanks.

I actually liked the extreme of it, however, can understand why it can skew the results. :)

But yes, from what I've been experiencing with my own folds, it won't be too easy to have a low DDG and a high CS. Hopefully people will remember to still pay close attention to their other objectives (ie Core Existence and BUNS)

Joined: 12/06/2008
Groups: Contenders
At what point do the DDG and CS values become meaningless?

I was able to continue working on 1920 simply by re-booting the game. No hang-ups since.

I'm still working the puzzle, because I have a good, stable design with four hydrogen bonds to the target. The DDG is currently at -39.3, and the SC is currently at 538.

The top-scoring solution has what is obviously an incorrectly high set of objective scores. Mine are higher than I thought I might get for the configuration, and they are still improving via a script. But are my scores also invalid? Am I wasting my time using the script, when the base score (current score minus DDG and SC bonuses) is increasing very little?

Which is more important, now? Minimizing total energy? Or maximizing objective values?

bkoep's picture
User offline. Last seen 6 hours 25 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

If you've found a solution that meets the Objective thresholds, then you should focus on the base score (or even better, start a brand new solution).

It's not clear to us that there are benefits in improving the Objective values beyond the target threshold (DDG < -40 and Contact > 400). We had intended for the Objective bonuses to plateau so that there would be no incentive for pursuing extreme Objective values. There is an error in this puzzle that allows the Contact Surface bonus to keep increasing after you pass 400; we'll be sure to correct this in future puzzles.

With your DDG and Contact values, there's no need to keep improving them. We would much prefer to have 2 solutions with DDG=-40 and Contact=400; rather than just one solution with DDG=-50 and Contact=600.

alcor29's picture
User offline. Last seen 14 hours 56 min ago. Offline
Joined: 11/16/2012
Hard to do

Not just slow, but hanging and crashing. and other weird things. May have to give up on it.

bkoep's picture
User offline. Last seen 6 hours 25 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Thanks for the feedback

If you have more details that can help us reproduce hangs and crashes, that is always helpful!

Joined: 12/06/2008
Groups: Contenders
Puzzle is hanging up on

Puzzle is hanging up on random actions: one time for a mutate, one time for a sidechain wiggle, one time for a backbone wiggle. Three hang-ups in fifteen minutes. VERY annoying.

Joined: 12/06/2008
Groups: Contenders
And... now it locked up when

And... now it locked up when I initiated a script.

Moving on to 1918b and 1919, until the hang-up problem is fixed.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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