Spring 2019 Science Chat!

Science Chat April 10th in veteran chat

Join the Foldit team for a chat about the science behind recent Foldit puzzles! If you leave questions in the comments below, we can prepare some answers in advance to help move the discussion along!

Date: Wednesday, April 10th, 2019
Time: 9pm GMT; 1pm Pacific Time Zone
Location: #veteran chat


(Thu, 04/04/2019 - 18:18  |  9 comments)
Joined: 04/28/2015
Groups: Go Science
When will there be a deep

When will there be a deep introduction of artificial intelligence and a complete base of all 3D structures?
Professionals of deep learning, who won first place at Casp - say that they cooperate with the baker laboratory on this topic. When will there be a fundamental change?

Joined: 06/06/2013
Groups: Gargleblasters
symmetry monomer rotation -- I want my legos

I find that I can not rotate the pieces of a monomer in any direction I want relative to the symmetric pieces. Is this a design intent, or a software limitation? for example, even from the start you can not orient the 2 lines of a dimer in parallel. They always flip to opposite directions (e.g. one north and one south). I feel like my lego pieces have taken on a mind of their own

Old dell machine, windows 7

jeff101's picture
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Try using bands

Have you tried the following?
Freeze both strands,
add a band from strand A residue 1 to strand B residue 1,
add another band from strand A residue N to strand B residue N,
and then wiggle the result.

If you want the opposite orientation, do as below instead.
Freeze both strands,
add a band from strand A residue 1 to strand B residue N,
add another band from strand A residue N to strand B residue 1,
and then wiggle the result.

bkoep's picture
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Should be possible

Hmm, it should be possible to accomplish what you want.

In a symmetric dimer puzzle (with C2 symmetry), there are different ways to align the two chains with respect to the symmetric axis.

For example, consider if you make a single long "megahelix" with the active copy. Then you should be able to align the symmetric megahelices in a parallel, head-to-head fashion (when the symmetric axis is parallel to the megahelix); or, you could align the helices in an anti-parallel, head-to-tail fashion (when the symmetric axis is perpindicular to the megahelix).

I think you should be able to accomplish this by rotating the pieces with the Move tool (the purple arrows). Or, as jeff101 suggests, try banding the pieces that you would like to be adjacent (head-to-head, or head-to-tail).

If that still isn't working, it's possible there is a software bug. In that case, some more feedback would be helpful. Maybe a screenshot with bands between the residues that you would like to be adjacent?

spvincent's picture
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I believe the issue here is

I believe the issue here is that there are more ways of arranging the two chains than can be described by rotation about an axis: you need to be able to (possibly among other things) translate along that axis too.

Sorry I'm having problems attaching an image (Ubuntu) but have scientist-shared a couple of solutions that I hope illustrate the problem. The names are symmetric dimer issue 1 and symmetric dimer issue 2.

bkoep's picture
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Cyclic vs. helical symmetry

Aha, I see what you mean! Thank you for sharing! Below is a screenshot with one of your examples (I unfolded one of the helices to clarify where the symmetry axis is). What you'd like to do is not possible in the puzzle, and this is intended behavior.

In this case, it sounds like you'd want to move the active subunit (right) slightly up, while moving the symmetric subunit (left) slightly down. Unfortunately, this operation would break the cyclic symmetry.

This puzzle (Puzzle 1658) has C2 cyclic symmetry, which means that symmetric copy is rotated 180 degrees about the symmetric axis (in the screenshot, this axis runs vertically down the center of the screen). If we carried out the operation to satisfy your bands, then the symmetric copy would be rotated 180 degrees about the axis and translated along that axis. This would be a "helical symmetry" (or "screw symmetry"), which is distinctly different from C2 cyclic symmetry.

Helical symmetry exists in biological proteins (e.g. see tubulin). But the helical symmetry usually means that copies can continue to assemble along the symmetry axis, so these proteins form fibers. For now, we are just interested in designing proteins with cyclic symmetry—but one day we may try helical symmetry in Foldit!

Recently, some other members of the Baker lab designed protein fibers with helical symmetry (you can find a PDF of this paper on the Baker lab website).

robgee's picture
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Is there anything you can say about aflatoxin:
Have the foldit results produced anything interesting?
Are the foldit results of any value in any way?
Are you brewing up results in the lab ?

Susume's picture
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Beta Barrel designs

In 2018 the Baker lab had two publications about the first successful denovo designs of beta barrel proteins using Rosetta. Foldit players have also submitted a variety of beta barrel designs: have any foldit barrels been successful in Rosetta testing?

Joined: 12/13/2015
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monomer unit core

In symmetry puzzles there is a core existence filter ensuring that each monomer unit has an individual core. But there are some structures in PDB in which monomer units lack their own core or have only a small part involved in it (for example 5Z1O, 4S37 and 4OSD). How do such proteins fold and is it feasible to try to design such structures in foldit?

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