Through the eyes of a scientist: Part 2 - Puzzle 1052

Embedded Video: 

Join Baker Lab scientist bkoep for an in-depth look at some Foldit player-designs from puzzle 1052: 80 Residue Symmetric Trimer Design!

In addition to highlighting some of our favorite Scientist-Shared solutions, we'll look at several lower-scoring designs to illustrate issues relating to:

  • hydrogen bond networks
  • buried, unsatisfied polar atoms

Check it out and leave your questions in the comments below!

( Posted by  bkoep 76 864  |  Sat, 02/28/2015 - 00:25  |  12 comments )
2
Joined: 10/30/2012
Groups: Beta Folders
this fits with a lot of the

this fits with a lot of the comments on 1054, a lot of us noticed we not able to keep the ligand in a position that maintained the hydrogen bonds. it was extremely frustrating to watch your bonds be broken as your score went up.

so it was encouraging to hear that hydrogen bonds might be scored in the future.

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Hydrogen bond scoring

To be clear, hydrogen bonds are scored in Foldit, and contribute (often substantially) to the total score of a good model.

At an interface, however, Foldit favors hydrophobic side chains because they contribute to stronger binding, and hydrogen bonds simply do not contribute enough energy to counteract this bias. What we want to implement is a special bonus for hydrogen bond networks at the interface, so that we can properly encourage specific interfaces—even though they aren't as strong.

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Thanks for this video bkoep:

Thanks for this video bkoep: it's great to get these insights into the pros and cons of different designs.

Joined: 06/17/2010
Looks like

we should first make "good" monomer witch phobic core and proper philic outside then find way to make it bond to itself.

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Nice feature.

It would be nice if we could disable the symmetric aspects of the game while designing the monomer so that it's not so cpu intensive during the beginning stages.

Joined: 09/24/2012
Groups: Go Science
good idea !

The monomer part of the game would also be easier to center and rotate on the screen.

btw thanks bkoep ! I find also encouraging that lower scored solutions still can be even more interesting than high scored ones. This encourage to share to scientists. It's also great that we got this "player solution" for further evolving in puzzle 1058. Quite a chalenge for our "evolver" skills.

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Good suggestion

I agree, it would be neat to switch symmetry on and off. Unfortunately, this is isn't as simple as it sounds, and we probably won't try to implement this anytime soon.

If players are finding the symmetric chains cumbersome, they can try moving the symmetric copies apart from one another, and adjusting the view so that only the active copy is visible. The overhead for using symmetry for scoring/wiggling/shaking is not actually very large (it should run about as fast as for a monomer)—I suspect a lot of the lag results from rendering the extra symmetric residues in the display.

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Can you turn off display of the monomer copies?

Why not have an option in the View Menu so folks can decide between showing all monomers or just the main one? If there is a way to do this already, please let us know.

Thanks!

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Probably not

I think the problem with this is that the active monomer would still "feel" the symmetric copies, and this might lead to some confusing behavior.

For example, imagine the frustrating scenario in which the Wiggle tool blows apart your solution for seemingly no reason—when in reality, the active monomer has severe clashes with the "invisible" copies.

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The player could control what is shown

I don't think it would be confusing, especially if the player knowingly chose not to show the copies. Having the copies hidden would let players examine the contact region more closely without the copied monomers blocking the view.

Perhaps having an option like show copied monomers as transparent would help. The copied monomers could display as white/grey/black outlines or a pulsed view so they would be partially visible but not obscure the view of the main monomer.

From your posts above, it sounds like it would be easier to change the display of the copied monomers than to actually turn off the calculation of their behavior.

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Simpler views render more quickly

You also imply above that rendering the copied monomers may account for some of the lag in symmetry puzzles. If you let the copied monomers be invisible, they should take no time to render, and this should help the symmetry puzzles run faster.

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symmetric puzzle import from non symmetric?

Would it be possible to do it with import? I.e. release two versions of a puzzle: monomer and symmetric that we could import/export between?

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