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I was wondering if we can have copies in pdb format of the top-scoring

proteins and proteins that you use in the lab to try our own experiments on?

Thank you

LociOiling's picture
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Joined: 12/27/2012
Groups: Beta Folders
frequently asked question

This question is related to the "why isn't Foldit open source?" that comes up most often.

The short answer is that you don't get your protein back as a PDB, except in rare cases.

Over under terms and conditions, you'll find this:

Scientific discoveries will be made publicly available and the host institution(s) will handle ownership of discoveries. All significant scientific discoveries (e.g. structures, algorithms, etc) made in the game will be made publicly available. In the event that some discoveries may warrant patent protection, the host institution(s) may (but are not obligated to) handle the patent application process. Individual players who contributed to the discovery will be considered co-inventors for any discovery produced through play. Data logs of player activity will assist in determination of attribution. Individual puzzles may specify further clarifications to this policy.

So the host institutions you see on the Foldit splash screen control the results and decide what's a significant scientific discovery. And of course any discovery must have a published paper, and probably one or more PDB entries.

In the PDB, structure 3SQF if the Mason-Pfizer monkey virus (M-PMV), and you'll see "Foldit Contenders" as one of the authors, referring to the Contenders group. the Mason-Pfizer Monkey Virus page on the wiki gives a little bit more background.

3UOS is another early success, a redesigned Diels-Alderase enzyme, with "Players, F." (Foldit Players) as an author on the paper.

A few proteins designed from scratch by Foldit players have been "solved" just like natural proteins and had their results published. See solved Foldit designs on the wiki for the short list, currently four proteins. There are some more in the pipeline, but not yet published.

I may have missed some results, but that's the general drift. You can certainly make screenshots of your protein, and recipes like print protein capture the primary structure and lots of other details, but you don't get a PDB.

It'd be nice to have mini-PDB of our own, but I don't think that's going to happen. Aside from the intellectual property issues, the scientists also have a concern about the "diversity of solutions" and outright "copying" of proteins. In other words, Ferredog-Diesel (also known as 6NUK) is great, but they'd like you to come up with something different.

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