bkoep's picture
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Objectives

Buried Unsats (max +500)
Detects polar atoms that cannot make hydrogen bonds. Note that the frozen target includes 8 buried unsats that may be impossible for players to satisfy.

Residue Count (max +275)
Penalizes extra residues inserted beyond the 177, at a cost of 55 points per residue. Players may use up to 182 residues in total.

Core Existence (max +2400)
Ensures that at least 25 percent of residues are buried in the core of the monomer unit.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

jacob_n's picture
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Cysteine bridges?

Are cysteine bridges an option for this puzzle?

bkoep's picture
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Possible

You can design disulfide bonds into your protein, and they might help stabilize your protein. But we do not think disulfides are necessary, and Foldit will not reward these with a score bonus.

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Where are the sugars?

The coronavirus spike protein is supposed to be a glycoprotein. So why aren't we seeing any sugars in the locked region?

Joined: 06/24/2008
Groups: Void Crushers
sugars

Foldit gods used the sugars in their morning coffee.

Joined: 08/11/2010
Do tell! :-)

Do tell! :-)

bkoep's picture
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Great question!

Fortunately there are no sugars on this part of the spike protein. These puzzles use only the receptor-binding domain (RBD) of the spike protein—the part the interacts with the human receptor.

The rest of the spike protein is much larger, and much of it is covered with such sugars. Because the sugars are polar and "floppier" than protein side chains, it would be much harder to design a protein that sticks to a glycosylated region of the spike protein. In that sense, we are lucky that the RBD region is not glycosylated.

grogar7's picture
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500 maximum for buried polars filter?

The puzzle comments indicate 500 points maximum for buried polars filter, but I have 550 points (7 buried polars). I cannot seem to load an image here. Will share with scientists.

bkoep's picture
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Target BUNS

That's great! You must have found a way to satisfy one of the BUNS atoms on the target.

grogar7's picture
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problem with Buried Polars filter

I have noticed that moving the designed protein well away from the target (so there is no interaction with the target) and simply rotating it with the move tool will change the number of buried polars. Explanation?

bkoep's picture
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Surface area approximations

This is not surprising, and has to do with some technical details of the BUNS calculation.

To detect whether a polar atom can make H-bonds with surrounding water, we need to calculate how much of that atom's "surface" is exposed. To calculate this exactly is slow to do; to speed things up, we use an approximation that involves slicing the protein into a 3D grid of voxels. This method is much faster, but is also a little unstable, because simple rotations and translations affect how the protein aligns to that 3D grid.

We are exploring ways to avoid this approximation, but these will probably make the BUNS objective slower to compute.

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I just saved my 1843 solution

I just saved my 1843 solution from the main client with 10 BUNS, and loading it in the devprev client resulted in 13 BUNS, and a lower score.

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Thanks, bkoep

Thanks, bkoep, for your replies to my concerns above. Especially interesting are the Surface Area approximations and the implications for score when this filter is active.

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