puzzle picture
482: Advanced Alignment Puzzle
Status: Closed


Name: 482: Advanced Alignment Puzzle
Status: Closed
Created: 11/16/2011
Points: 100
Expired: 11/25/2011 - 03:00
Difficulty: Advanced
Description: This advanced puzzle requires using the Alignment Tool. There is only one template you can thread with, but unfortunately the alignment is incorrect. You will need to master Intro Puzzles 6-1 through 6-3 to succeed in this puzzle. Make sure to move the alignment around and try to help Foldit resolve the gaps in the alignment (see puzzle comments for tips).
Categories: Overall, Prediction

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Joined: 05/09/2008
Groups: None
Starting Alignment is incorrect

We know the starting alignment is wrong, you might even have trouble threading it at all:

In the above screenshot, Foldit cannot resolve the gap between the red R and the D, therefore the alignment needs to be moved around so that Foldit is able to thread the sequence onto the template.

Joined: 09/22/2011
Groups: None
Do we have a server structure

Do we have a server structure prediction for this one ?

Joined: 05/09/2008
Groups: None
we can post this puzzle using server predictions later

If you feel that would be useful, we can post server predictions for this one.
The best servers will most likely use this exact template, so we're hoping the Alignment Tool can get the job done.
I'll get server predictions ready for this one so we can repost the puzzle if needed.

Joined: 09/22/2011
Groups: None
My bad

What I actually meant was SAM prediction, I should have been more specific.

Joined: 05/09/2008
Groups: None
ah... no problem!

We'll repost this one as a quick puzzle with the secondary structure predictions from the SAM server.

Joined: 09/22/2011
Groups: None
Thank You

I find those very helpful whenever the puzzle is not a very close match, or when the shape is not well defined. I would actually like to request that we get them with all of the CASP puzzles this time around as well, since many times it is helpful to have a rough guide of where to explore variations in the protein. Especially when combined with server predictions or similar proteins to thread from, they really help to visualize where changes may need to be made to improve a structure.

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Joined: 08/05/2010
Groups: Void Crushers
tutorials or video from this?

It would help the newer players who were not around when the alignment tool was implemented for this puzzle alignment solution and subsequent state to be shown as a video. The current tutorial is very basic.
I can do 7 layer phylo sequences easily but the connection between clicking on the actual puzzle and the letter alignment I find quite baffling. And yes I have read the instructions and watched the existing video. thanks

Joined: 05/09/2008
Groups: None
good idea spmm

We should definitely make a tutorial video using this example since the initial alignment is clearly wrong.
Once this puzzle is closed (and some of you have been able to correctly move the alignment around) remind me (feel free to PM me about this) to make a video of those correct moves.

Thanks for the great suggestion!

Joined: 09/19/2011
Groups: Beta Folders
More info can be found on the comments section of the wiki

The Contenders did a great job with this puzzle and infjamc gave me permission to repost a response from him to me. It is very informative and can be found at the following link:


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