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Joined: 12/03/2020
Groups: None

I am new - can I fold my own sequence de novo locally? Just for my own curiosity?
And second: can I make disulfide bonds?

Best regards,

Alar Aints

Joined: 12/27/2012
Groups: Beta Folders
yes, and yes

Check out the "Protein Design Sandbox" puzzle that you'll find if you scroll down in the "Science Puzzles" list. The "sandbox" part means the puzzle doesn't award any points, but it gives you lots of flexibility in creating a design. You're still limited to just a single chain of amino acids, but otherwise there are few restrictions. Also, it currently has 1,577 days left, so plenty of time to try things.

Right now, the regular design puzzles (where you play for points) are focused on binder designs. There may still be "monomer" (single chain) or "symmetry" (multiple identical chains) free design puzzles from time to time. The binder puzzles and the free design puzzles impose various restrictions various types of "objectives", which add or subtract points (and slow things down), so these puzzles aren't totally "free". The "Protein Design Sandbox" has just "core existence" and "ideal loops" objectives, and I don't think they give a bonus or penalty.

As far as disulfides, design puzzles often don't allow cysteine, but again "Protein Design Sandbox" doesn't have that limitation. Many of the puzzles in the "revisiting" series can have disulfide bridges, although not this week. Turn on "show bonds (sidechain)" under "View" to see the bridges. They show up as a yellow/green spiral, similar to the blue/white spiral for hydrogen bonds. Other view options, like "show sidechains (all)" and "CPK" or "EnzDes" coloring make it easy to spot the cysteines, highlighting the sulfur atom at the tip of the sidechain in yellow.

Joined: 06/14/2021
Groups: None
Hey, new as well. If You

Hey, new as well.
If You don't mind: why do they often not allow cysteine?

(Also: what's the best place to post when Foldit crashes during the log-in?)

jeff101's picture
User offline. Last seen 14 hours 14 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Why forbid cysteines?
My sense is that designed proteins containing 
cysteines or disulfide bonds are harder to 
synthesize and test in the lab.
Joined: 12/27/2012
Groups: Beta Folders

When you crash, go in the Foldit directory (c:\Foldit or whatever) and check log.txt. There may also be a debug.txt.

The log.txt file sometimes has usable "traceback" info at the end of the file. The traceback at least says what was calling what at the time of the crash. You'll often get a debug.txt in this case.

Sometimes, the traceback consists of all zeroes, or you'll just see an "error initializing symbols" error. This kind of log file is probably not going to help, but there's a small chance it contains some useful information.

The easiest way to upload log.txt is to get on the Foldit Discord server, and go to the bugs-and-feedback channel. You can just drag log.txt there and drop it, then add a comment saying what you we're doing when the crash hit.

If there's a debug.txt, it gets uploaded automatically, so you don't have to worry about that.

The other way to upload log.txt is to post a feedback in here on the fold.it site. The only drawback to feeback is that you must open your feedback, then attach log.txt and whatever in a separate reply to the feedback post. Somehow the ability to attach files to the original post got lost a while back, and nobody knows how to fix it.

The Foldit team is working on a whole new website, so in theory it will have a better system.

Just an aside on the website issues, uploading images has been broken for a long while, but I see that HuubR has successfully added images to a new feedback. So maybe something has been fixed, some further investigation is needed.


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, Boehringer Ingelheim, RosettaCommons