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Joined: 05/28/2012
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I'm a new foldit player and I was looking at some tutorials and such. I noticed most of the tutorials have things to do with going into structure mode and changing things. This makes me wonder, does that change the protein's chemical makeup? And if it does, then don't structure changes make the puzzle completely useless when trying to find the correct folded structure?

Another question I have is about the CASP puzzles. We aren't supposed to be changing things in the alignment, are we?

beta_helix's picture
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We don't know what the correct fold is.

Hi CoolgyFurlough.

The main issue is that we don't know what the correct folded structure looks like, this is what we're trying to predict.

The CASP puzzles are proteins that will soon be solved, but haven't been released yet. So you can imagine that a region in one of these proteins could be a helix or sheet or loop, we just don't know. That is why the best method is to try out all three and hopefully the Foldit score will be able to tell you which structural change is most favorable.

As for the alignment tool, we are giving you alignments to templates but indeed those alignments could be off. A perfect example of this was the first CASP10 target (T0644) where the default alignment (that was also used by Rosetta) had a register shift.

You can see videos about both this register shift and a tutorial on Alignment Tool basics in our YouTube Channel:

http://www.youtube.com/user/uwfoldit

Welcome to Foldit!

Joined: 05/28/2012
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Thanks

Thank you for answering my question. I think this game is extremely fun (and crack in digital form) but I like to take it as seriously as possible so that I can contribute.

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