1918b: Designable Linker: Coronavirus Spike Binder

Closed since over 5 years ago

Summary

• Created: November 19, 2020
• Expires: November 25, 2020 at 23:00 UTC
• Max points: 100

Description

Note: This puzzle replaces Puzzle 1918, which had some scoring problems. Unfortunately, players may not load solutions from the original Puzzle 1918.



This is the third puzzle in the designable linker series! We are providing parts of two of the best-known designed binders to the SARS-CoV-2 spike, and are challenging players to link them together with a rigid linker! The two helical bundles are the parts of the two binders. They are currently connected with a flexible alanine linker that needs to be redesigned. We have also included the parts of the actual spike that are within 15 angstroms of the termini of the binders, so you know what regions your binder has to avoid to prevent clashing. The PDB has a slightly different configuration from previous puzzles. The absence of the helices will give more flexibility in any designed linkers.

Top groups

• 1. Go Science 100 pts. 21,547
• 2. Gargleblasters 73 pts. 21,533
• 3. Contenders 52 pts. 21,390
• 4. Anthropic Dreams 36 pts. 21,340
• 5. Void Crushers 24 pts. 20,741
• 6. Beta Folders 16 pts. 20,732
• 7. L'Alliance Francophone 10 pts. 20,359
• 8. Marvin's bunch 6 pts. 20,347
• 9. BOINC@Poland 4 pts. 20,007
• 10. Hold My Beer 2 pts. 19,705

Top soloists

• 1. ZeroLeak7 100 pts. 21,536
• 2. Enzyme 98 pts. 21,533
• 3. dcrwheeler 95 pts. 21,442
• 4. ichwilldiesennamen 92 pts. 21,406
• 5. mirp 89 pts. 21,357
• 6. phi16 86 pts. 21,340
• 7. grogar7 84 pts. 21,317
• 8. spvincent 81 pts. 21,308
• 9. akaaka 79 pts. 21,297
• 10. Mike Lewis 76 pts. 21,289

Comments

[Formula350]

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 205, at a cost of 55 points per residue. Players may use up to 215 residues in total.

Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

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

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.


EDIT: FULL DISCLOSURE - I changed the wording from:
"Penalizes all CYS residues."
… to:
"Prohibits CYS residues."
Reason: We are not allowed to mutate in Cysteine and therefore, by definition, we aren't able to be "Penalized" for using it since we are unable to use it; thus, my swapping of it for "Prohibits".

[Bletchley Park]

@bkoep, Why is a member of a competing team posting the objectives where this should be done by an official member of Foldit staff ?
This suggests credibility in an official position where this is not the case.

[bkoep]

Sorry, Bletchley Park. We've got our hands full and forgot to post the Objectives comment when we reposted this puzzle. I'm guessing that Formula350 simply copied the Objectives details from the original puzzle. In any case, the info seems to be correct.

I appreciate Formula350 helping out, and I don't want to discourage players from commenting with info that others might find useful. I do agree some context might improve clarity here (e.g. adding the phrase "Copied from original puzzle comments…" somewhere with the objective details).

[Formula350]

Sorry for the mix-up :)

[APPAAP]

Does anyone know why in the one of the two frozen a-helices (the second one according to the segment numbers)there are clashes?