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1918b: Designable Linker: Coronavirus Spike Binder
Status: Closed


Name: 1918b: Designable Linker: Coronavirus Spike Binder
Status: Closed
Created: 11/18/2020
Points: 100
Expired: 11/25/2020 - 23:00
Difficulty: Intermediate
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.
Categories: Design, Overall

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Joined: 09/29/2016
Groups: Gargleblasters
Objectives - (Copy of bkoep's comment in original 1918 puzzle)

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".

Joined: 05/19/2009
Groups: Contenders

@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's picture
User offline. Last seen 17 hours 47 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

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).

Joined: 09/29/2016
Groups: Gargleblasters
No problem, and will do in the future.

Sorry for the mix-up :)

APPAAP's picture
User offline. Last seen 7 weeks 5 days ago. Offline
Joined: 04/25/2020
Groups: None

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

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