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[DEVPREV] Coronavirus Anti-inflammatory Design with Binder Metrics
Status: Closed

Summary

Name: [DEVPREV] Coronavirus Anti-inflammatory Design with Binder Metrics
Status: Closed
Created: 08/13/2020
Points: 0
Expired: 08/20/2020 - 23:00
Difficulty: Intermediate
Description: This is a clone of Puzzle 1877, with the addition of three new objectives for the DDG, SASA, and Shape Complementarity of your designed binder. Note that these objectives are VERY slow to compute, so you must run them manually from the Objectives dropdown panel. (In a future update, these objectives may run in the background automatically.) The new objectives do not award any bonus, and players may share solutions freely between this puzzle and the original Puzzle 1877.
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Comments

bkoep's picture
User offline. Last seen 3 hours 1 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 +100)
Penalizes 60 points for each polar atom that cannot make any H-bonds. Note that the frozen target includes 15 buried unsats that may be impossible to satisfy.

Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 151, at a cost of 55 points per residue. Players may use up to 156 residues in total.

Core Existence (max +1000)
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.

spdenne's picture
User offline. Last seen 36 min 20 sec ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
What's supposed to happen

What's supposed to happen when you click 'Run'? I get no feedback.

bkoep's picture
User offline. Last seen 3 hours 1 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Calculation displayed in dropdown

A second or two after you click "Run", some text should appear like "Calculated SC: 0.659".

In this puzzle the new Objectives will not award any bonuses or penalties, so your score will not change based on the binder Objectives. However, if you hover the cursor over the Objective, more text will pop up with details about the Objective (like the target value).

spdenne's picture
User offline. Last seen 36 min 20 sec ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
It's not working for me. If I

It's not working for me. If I disable SS Design, toggle all, run all, then click run on one of the three new disabled filters, I get SS Design re-disabled, and told its change in points, but most of the time clicking run gives me no response at all.

bkoep's picture
User offline. Last seen 3 hours 1 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Fix in progress

Thanks spdenne! This seems to be the same problem as reported in Feedback. Are you on Windows? There was an issue with the Windows devprev release, which was supposed to fix this problem. We are working on it now, and devprev should be updated later today!

spdenne's picture
User offline. Last seen 36 min 20 sec ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
Yes windows. Working now,

Yes windows. Working now, with the latest update.

Joined: 05/03/2009
Groups: Contenders
Not Working

Same situation for me too. Clicking Run does nothing. Toggle all to the off position, click Run, still nothing.

LociOiling's picture
User offline. Last seen 1 hour 31 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
another one...

DDG, SASA, and Shape Complementarity all show as disabled, nothing seems to change that.

Joined: 05/19/2009
Groups: Contenders
"This condition is not being

"This condition is not being run and is returning cached results". "Disabled" and pressing 'Run' advances the undo pointer, but nothing happens.

20200811-a21a4ef4e7-win_x86-devprev

Joined: 06/24/2008
Groups: Void Crushers
not working

It is not woking on my MAC - I get no feedback or score

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

Working now

Now I have to read what they mean

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

Are they so demanding that they can not be run while Foldit runs?

bkoep's picture
User offline. Last seen 3 hours 1 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Work in progress

Yes, if we were to calculate these just like other Objectives, then Foldit would freeze up for a full second after every mouse click that changes your solution.

We are currently reworking some things so that these binder Objectives can run in the background, likely this will be in the next update. The objectives will not be any faster, and automated tools like Wiggle and Shake will take longer to run. But at least Foldit will not freeze up when these Objectives are enabled, and the program will still be responsive while they are calculating in the background.

Joined: 06/24/2008
Groups: Void Crushers
DDG score

So is the DDG target -40.0 or less or -40e+07????

LociOiling's picture
User offline. Last seen 1 hour 31 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
working on current devprev

On 20200817-087bbc0dad-win_x86-devprev, the new metrics are working, but it's a little quirky.

If you click "Run All" at the top, there's a long pause, and the scores for the three metrics are displayed. The scores persist until some part of the protein moves.

If you click "Run" for a single condition, there's a medium pause, and the score for that condition is displayed. The scores for the other two conditions are blanked out.

The new conditions don't have the usual "Enabled" checkbox, so you must click "Run All" or "Run" to get the scores.

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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