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1840: Coronavirus Anti-inflammatory Design: Round 4
Status: Closed

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bkoep's picture
User offline. Last seen 8 hours 7 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Detects polar atoms that cannot make hydrogen 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.

MrZanav's picture
User offline. Last seen 10 hours 45 min ago. Offline
Joined: 12/29/2018
Um

Is this puzzle supposed to be at a score of 177912?

bkoep's picture
User offline. Last seen 8 hours 7 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Yes!

Solutions from this puzzle will register extremely high Foldit scores. Usually, we try to correct the baseline score for each puzzle so that all puzzles score in the same range. But there was a mistake when we set up this puzzle, so the baseline score is much higher than normal.

This shouldn't affect gameplay or rankings. A lead of +500 pts here is equivalent to a lead of +500 pts in any other puzzle.

Joined: 09/24/2012
Groups: Go Science
Incorrect score function

303658 pts credited
Total of all subscores: -1511 pts
Total of all subscores + 8000: 6488 pts

Discrepancy: 297170 pts
Folter Bonus: 2170 pts.

On the locked protein, there are many "O points" segments, other with positive points, many with negative points.

Calculated with:

https://fold.it/portal/recipe/102018

Verified with:
https://fold.it/portal/recipe/100420

Moreover, I see >25 players and 9 groups with 306,XXX pts. It's quite uncomon to see players scores within top 0.3% range at start game.

OWM3's picture
User offline. Last seen 48 min 13 sec ago. Offline
Joined: 03/08/2020
Groups: Gargleblasters
Segfaults

I left 4 instances for a night with 4 different recipes. And all instances crashed during the night with 3 completely different error messages.

LociOiling's picture
User offline. Last seen 41 min 50 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
See this feedback...

puzzle 1840 crashes and evoed solutions cannot be uploaded describes what may be a similar problem.

Right after a crash, the file log.txt in your Foldit directory may contain clues. Please consider attaching a log.txt in a reply to the feedback above. At the very least, it will identify which platform you're on.

There may also be traceback information in log.txt pointing to the source of the crash. On Windows, however, the traceback often appears to have be zeroed out.

When you restart Foldit, log.txt is overwritten, so any evidence is lost.

When you create a feedback, the Foldit website doesn't allow you to attach files. (No one knows why.) Replies to an existing feedback allow attachments, however. So you can always create a feedback, then reply to yourself with any attachments.

In addition to log.txt, the file debug.txt is sometimes generated by a crash. This file uses a properties file format, and contains the traceback and some more context. There's a timestamp and some identification of what Foldit was doing.

Unlike log.txt, debug.txt is not overwritten when you restart Foldit. It may or may not be overwritten by the next crash. Unfortunately, the debug.txt timestamp is in seconds, so it's a little hard to decipher. Check the file's creation time on your system to make sure it was created by the crash in question.

I had thought that debug.txt was supposed to be uploaded automatically, but if so, it's not clear that it's useful to the Foldit team. Still, it can't hurt to attach it to a feedback.

LociOiling's picture
User offline. Last seen 41 min 50 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
using multiple directories may also help...

I strongly recommend running each Foldit client from a separate directory (folder).

Multiple Foldit Clients on the wiki describes how to set this up this configuration on different platforms.

Among other things, this setup means each client will have its own log.txt (and potentially, its own debug.txt).

You also don't have to worry about the track name this way, so each client can have it's own scriptlog.default.xml and its own automatic saves in the default track.

Long long ago, the multiple directory approach seemed to reduce the number of crashes on Windows. Foldit crashed a lot in those days.

On Windows, you can just copy C:\Foldit to make c:\Foldit1, c:\Foldit2, c:\Foldit3, and so on. Then you'll need to make shortcuts to foldit.exe in each of these directories to run the clients.

I've also added custom icons for each client. See my video Running Foldit in Multiclients (for Windows) for a detailed look at the process.

grogar7's picture
User offline. Last seen 2 hours 28 min ago. Offline
Joined: 10/03/2011
no cytokine helix fragment

The puzzle description says an helix fragment from IL6 cytokine is included in the protein to be designed. That is not the case. The designable protein is presented as a denovo strand.

bkoep's picture
User offline. Last seen 8 hours 7 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good catch!

That's a mistake in the the puzzle description, which I've just edited.

Joined: 12/06/2008
Groups: Contenders
No ALA in helices?

Alanine is one of the most common AAs in helices. Why is it forbidden in helices in this puzzle?

bkoep's picture
User offline. Last seen 8 hours 7 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
An imperfect solution

Sorry I didn't see this comment before the puzzle closed!

The problem we are trying to avoid is excessive alanine. Foldit players discovered that you can pack helices really tightly using exclusively ALA. The tight packing gives really high Foldit scores, but we don't expect these designs to fold as well as designs with better "interdigitation" between sidechains in the core.

Ideally, we would put a soft limit on the amount of ALA allowed in designs (it's on our to-do list). In the meantime, we found that we can get by without ALA in secondary structure, and it seems that Foldit players can design super-stable proteins without any ALA at all.

irk-ele's picture
User offline. Last seen 5 weeks 1 day ago. Offline
Joined: 05/07/2020
Groups: None
Further Improvement

Dear scientists, just now I used "upload to scientists" to share another huge bonding improvement to my previously uploaded suggested solutions. Now, there is a total of 2/3 hydrophobic interactions (depending on which of my solutions you look at), 3 hydrogen bonds and 2 satisfied BUNS all within the target, which I think make it a very strong and possible binder.

Otherwise, as I am fairly new to this subject, I would highly appreciate it if you could have a look at it and give me feedback (Am I even on the right track?), either here or via mail or whatever possibilities there are.

Is there a place to share and discuss such topics with other players?

Thank you very much.

Joined: 11/05/2019
Groups: Foldit Staff
Feedback

Hi Irk-ele!

Feel free to join the Foldit discord to share and discuss topics with other players and developers.
https://discord.com/invite/Ffgx2KJ
Please let me know if you have any additional questions.

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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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