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1859: Coronavirus Anti-inflammatory Design: Round 7
Status: Closed


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bkoep's picture
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Buried Unsats (max +100)
Penalizes 60 points for each polar atom that cannot make any H-bonds. Note that the frozen target includes 15 buried unsats that may be impossible to satisfy.

Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 151, at a cost of 55 points per residue. Players may use up to 156 residues in total.

Core Existence (max +1000)
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.

Joined: 09/24/2012
Groups: Go Science
Why no core existence Complex?

I've a problem with the new Buried Unsats filter. The protein tends to disassemble (because there are less buried unsats when the monomers are separated).

Ther should be a core existence complex filter (or wathever) in order to counter this problem.

bkoep's picture
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Avoid BUNS

I think this is working as intended. If BUNS are created when the symmetric copies come together, that means your complex is unlikely to assemble--no matter what the core complex looks like. It's more important to focus on satisfying BUNS than increasing the complex core.

Joined: 04/02/2020
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Speaking of BUNS

They are not capped in this puzzle. Satisfying target BUNS adds 60 points to the total of bonus points.

But more importantly, if I satisfy target BUNS manually and then wiggle it a bit, it sometimes happens that it "removes" those satisfied BUNS.

Does that mean, it is not stable/sticky enough or how do I have to interpret this behavior?

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Hi there! Thank you so much for your question--I have passed it along to the team.

bkoep's picture
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Problem with Wiggle

Yes sometimes Wiggle will create BUNS that you've manually satisfied. This is not a problem with the stability/stickiness of your solution. It is a problem with Wiggle, and unfortunately it is not an easy problem to solve.

Under the hood, Wiggle tries to improve your score by optimizing lots of different score terms at once (like clashing, H-bonding, and backbone geometry). However, Wiggle doesn't know about BUNS. This means that sometimes Wiggle will sometimes cause new BUNS problems while it is trying to optimize the other score terms.

This is a tricky problem to solve. Since the BUNS Objective is not continuous (there's no such thing as 1.2 BUNS), it is not compatible with Wiggle. My best recommendation is to try adding bands to keep BUNS satisfied.

Joined: 04/02/2020
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Thank you

For the explanation and the suggestion.

Joined: 09/24/2012
Groups: Go Science

freeze the related sidechain or even segment

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