Create hoops (like bands, but the protein can slide through them)

Case number:845813-992670
Topic:Game: Tools
Opened by:jeff101
Opened on:Tuesday, May 15, 2012 - 05:13
Last modified:Wednesday, August 22, 2012 - 08:39

It would be nice if there was a new thing in Foldit, like a band, but called a hoop.
Each hoop would be a fixed position in space that the protein needs to thread itself through.
It would be nice if the user could lay out a series of such hoops on the screen
and be able to reposition these in 3D space, sort of like Foldit allows with bands right now.
Once the hoops are in place, the user could assign each one a unique number.
Then the user could apply a band to segment 1 of the protein to fix it in place.
Next, the user could run a command called something like "worm"
that will thread the loose end of the protein through the lowest-numbered hoop
and then try to thread the rest of the protein through all the other hoops in ascending order.
If the protein isn't long enough to pass through every hoop, that is ok.
The protein will just end sort of aimed between the highest-numbered hoop it passed through
and the hoop it would go to next if the protein were longer.

Hoops would help in puzzles like #547 where you are trying to match certain known density patterns.
If you don't like how the protein fits itself onto the path of the hoops, you could move some hoops,
remove some, or even add more hoops, and then try the "worm" command again.
You could also move the band holding down segment 1
to adjust which segment (amino acid) of the protein comes closest to each hoop.
You could also add another band to the other end of the protein
to create a sort of tug-of-war between the ends,
loosening or tightening the entire protein and how it fits through all the hoops.

Hoops would be different from bands
because they would not be bound to specific amino acids on the protein.
Instead, they would be like fixed positions the protein has to slide itself through
when the "worm" command is executed.

(Tue, 05/15/2012 - 05:13  |  8 comments)

spmm's picture
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jeff perhaps you would enjoy actually playing the game if you spent some time doing it - consider your suggestion and define how it would work - ├Żou could perhaps create a tunnel with the hoops - however you need to work out how the backbone segments are rotated and bonded - also the real life electron density puzzles are less simple.

For me I just do that in my head and simply adjust the protein itself rather than introducing another layer of construct which may or may not be useful.

Joined: 06/17/2010
Status: Open » Closed

Freeze/lock in space feature request posted already.
Marking as duplicate to:

jeff101's picture
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I have read the post several times, but I still don't think it is exactly the same as what I am proposing here.

The hoops I propose here are more like pulleys or the eye of a needle. A hoop would provide a fixed point in space, but any part of the protein could pass through this point. If you pulled on the end of the protein, the protein would move like a rope or thread through the hoop, and which amino acid is closest to the hoop would keep changing.

You could think of the hoops as destinations within an itinerary for a trip through Europe. There could be hoops for London, Paris, Berlin, Geneva, Florence, and Athens. Jim (one conformation of the protein) could start in London on August 15, go to Paris on the 18th, to Berlin on the 21st, Geneva on the 24th, Florence on the 27th, and Athens on the 30th. Here the dates correspond to residue numbers within the protein. Mary (a different conformation of the protein) could start in London on August 13, go to Paris on the 16th, to Berlin on the 19th, Geneva on the 22nd, Florence on the 25th, and Athens on the 28th. Jim and Mary pass through the same destinations (hoops) but on different dates (different amino acids located at each hoop). By changing the starting date (position of the protein), you change which dates each destination is visited.

I hope this clarifies things.

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It would help to have something that would make the protein move like a snake, worm, or centipede. AA1 would move forward a short distance, then AA2 would move to where AA1 used to be, then AA3 would move to where AA2 was, etc. Then AA1 would move forward another short distance, AA2 would move to where AA1 was, AA3 would move to where AA2 was, etc. This process would keep repeating until AA1 completed moving through its desired path.

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+1 This sounds a lot like how the alignment tool works - the alignment template provides a path in space and you can slide all or part of the protein along it like beads on a string. The difference is that you could define the path yourself by placing the hoops, and then thread the protein to your user-defined path. If you find that you have put a proline in the middle of a helix, slide the beads along the path until the proline is in a better spot - without changing the overall shape of the protein. Combined with the cut tool, this could be a very powerful way to try different areas of the AA sequence in a given area of the shape you have in mind.

Joined: 08/29/2010

I think this should be implemented for the rebuild tool. You can create these hoops and then the new structure will be threaded through it! But i think i would only use this rebuilding the protein.

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There could also be two kinds of hoops: ones with no favored direction, and ones with a specified direction.

This way, if you want the protein to always go from left to right through a hoop as the residue number increases, you can use a hoop with a specified direction to enforce this. There could be an arrow symbol to show the specified direction of the hoop.

Also, if you don't care which way the protein goes through a hoop, you can use a hoop with no favored direction. Then, the protein could go through this hoop from left to right, right to left, into the screen, out of the screen, from top to bottom, from bottom to top, or any other direction.

Joined: 06/17/2010

It is similiar to my "aligment editor" idea - we draw a shape then thread it.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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