As a scientific/academic user, is it possible to incorporate another option "load my own protein to solve by fold it"

Case number:699969-995094
Topic:General
Opened by:rtseng123
Status:Open
Type:Suggestion
Opened on:Monday, May 6, 2013 - 02:09
Last modified:Thursday, August 14, 2014 - 12:54

Dear Fold it researchers,

I am a biochemistry graduate student at UC Merced. I would like to suggest another way to use fold it.

To allow scientific users to upload their own pdb file to visualize and fold on "fold it".

This fold it is a great platform to move protein and maybe improve structure by eye (with the help of rosetta energy function).

It will be great if it is possible to allow academic user to upload their own protein puzzle to solve on fold it too.

Thank you

Roger Tseng

(Mon, 05/06/2013 - 02:09  |  6 comments)


brow42's picture
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Hi Roger,

I've bumped your post down to 3. If there is an urgent time element involved, you should contact them directly.

There are several existing options. If you wish to use the Foldit client as a stand-alone visualization and optimization tool, you an obtain a stand-alone client from here: http://c4c.uwc4c.com/express_license_technologies/foldit . The stand-alone client allows you to import your own pdb files.

If you wish other players to fold your protein, you can open a contest and create a recipe that sets the protein to your sequence. You would have to recruit players to play your contest, however. If your protein is associated with an interesting scientific problem, you can request to have your protein turned into an official puzzle. BE ADVISED that players are frequently overloaded with puzzles, and Foldit has many puzzles they want to post but can only post a few at a time (by player request).

beta_helix's picture
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Thank you for the perfect reply, brow42.

And thank you for your question, Roger.

Indeed, you can find the academic version of Foldit (where you load in your own pdbs) here:
tinyurl.com/academic-foldit

If you have a Scientific problem that you think would be appropriate as a Foldit puzzle, we would be more than happy to talk with you about it. Just private message me.

marie_s's picture
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grofte's picture
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Could you please be a bit more explicit? I'm dumb.

Do I need to download and install Rosetta version 3.3 or is it also included in the most recent versions of Rosetta? How do I launch FoldIt after installing Rosetta?

Cheers

grofte's picture
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Just to give some detail: I've followed the link, obtained the license, downloaded and installed the latest version and now I don't know how to launch FoldIt or if it is even the right Rosetta version I have installed.

grofte's picture
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Update.
Found a Windows machine to run FoldIt standalone from the Rosetta 3.3 download. It runs and loads your structure but the interface is nothing like the current interface. It was basically useless. Don't waste your time.
If you need to do large scale rearrangements then I guess the best option is Coot and then low-temperature molecular dynamics. Preferably something coarse grained.

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