puzzle picture
1880: Coronavirus Binder Design: Round 16
Status: Closed

Groups

RankGroupScorePoints
1Gargleblasters14,812100
2Beta Folders14,78677
3Go Science14,71958
4Anthropic Dreams14,63343
5L'Alliance Francophone14,58131
6Contenders14,44722
7Marvin's bunch14,39715
8Void Crushers14,32711
9BOINC@Poland13,4667
10Hold My Beer13,2485
11Russian team12,9513
12SETI.Germany12,4322
13Team China12,0961
14FoldIt@Netherlands11,5101
15Italiani Al Lavoro11,2611
16Team Canada10,1681
17Cell Bio1,9311
18Minions of TWIS01
19Foldit Staff01
20Aalborghus01


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bkoep's picture
User offline. Last seen 2 hours 41 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Binder DDG
The binding energy of your design to the target. The target DDG is -40.0 or less.

Binder SASA
The solvent-accessible surface area that is lost upon binding. The target SASA is 1500 or more.

Binder Shape Complementarity
Measures how well your binder fits the contours of the target surface. The target Shape Complementarity is 0.60 or more.

Buried Unsats (max +20)
Penalizes 60 points for each polar atom that cannot make any hydrogen bonds. Note that the frozen target includes 8 buried unsats that may be impossible for players to satisfy.

Residue Count (max +275)
Penalizes extra residues inserted beyond the 177, at a cost of 55 points per residue. Players may use up to 182 residues in total.

Core Existence (max +2400)
Ensures that at least 25 percent of residues are buried in the core of the monomer unit.

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)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.

spmm's picture
User offline. Last seen 6 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
DDG - negative binding score

target is -40.0 or less - may be a bit counterintuitive for some sleepy folders :)

jeff101's picture
User offline. Last seen 1 hour 3 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
DDG

If the target DDG is -40.0 or less,
is a DDG of -60.0 better than -40.0, or
is a DDG of -20.0 better than -40.0 ?

https://fold.it/portal/node/2009115
says "A more negative DDG (or ΔΔG)
indicates stronger binding." Then it
gives an example where a Foldit design
with a DDG of -45.0 kcal/mol is
predicted to bind tighter than ACE2
with a DDG of -39.3 kcal/mol.

Joined: 12/06/2008
Groups: Contenders
I can't access this puzzle.

I can't access this puzzle. When I try to load it, I get the error message 'unused key bonus_coeff'.

Does this mean we are required to load the new update before we can play this puzzle? My two machines are currently in the middle of some long scripts I don't want to interrupt.

Joined: 09/29/2016
Groups: Gargleblasters
Yessir

For anyone else unable to get the puzzle to load, this

bkoep's picture
User offline. Last seen 2 hours 41 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Update required

Yes, the August 20 update is required to play Puzzle 1880.

Joined: 05/19/2009
Groups: Contenders
Baker lab already publishes working binders ?

I was surprised to accidentally find this publication on a series of apparently successful binder proteins coming from the Baker lab.

https://www.biorxiv.org/content/10.1101/2020.08.03.234914v1.full

Can you please elaborate on the findings ?

bkoep's picture
User offline. Last seen 2 hours 41 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
See Forum

Yes! Some Baker Lab scientists used computational methods to develop binders extremely quickly. These are very exciting results and we may dig into details in a later blog post.

There is also a forum discussion here.

Joined: 05/19/2009
Groups: Contenders
Would like to read more on the computational methods too !

Thank you for the quick answer and the link, I'm also very curious about the computational methods, can there please be a blog post on those too ? Is there a way we can improve / speedup our folding activities using computational methods as well ?

OWM3's picture
User offline. Last seen 39 min 54 sec ago. Offline
Joined: 03/08/2020
Groups: Gargleblasters
The Bug

Each time I press on "DDG Score" button - each time I get different values (from -18 to -20). If you want to debug this issue - I've shared a solution with 14363 points "for scientists".

Joined: 09/29/2016
Groups: Gargleblasters
Is it while you're Wiggling? -- UPDATED

Because if your protein is actively changing, even fractional points, running ANY of the New Metric filters is going to produce a different result.

For me, with no tool running, they all consistently reports the same score (even if ran individually).

To answer that for him, no he was not Wiggling. All he's doing is, with a "still" protein, pressing Run on DDG.

Since OWM and I are on the same team, I'm able to load his share.
I can confirm that for his pose, it does in fact churn out different results for DDG on almost ever Run.
My Tests: -18.8, -20.4, -18.8, -18.8, -19.2, *a few minutes later pressed again* -19.2, -18.9

SASA and SC do not vary. This also occurs when using Run All.

While I can't say I've personally ever ran the filters multiple times back to back on the same pose, I did try on my own design before loading OWM's, and mine did not exhibit this, only his Shared pose does.

Officially adding it to the internal Google Doc (my Community Crash Compendium) since it's reproducible on two systems, across different OS environments.

bkoep's picture
User offline. Last seen 2 hours 41 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good catch!

Good catch! There is a random component to the algorithm in the DDG Objective. In the future, we can simply turn off this random component, but in the long term we should probably try to come up a better non-random alternative for this component.

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