1918b: Designable Linker: Coronavirus Spike Binder

Summary

Name:

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

Rank

Group

Score

Points

Go Science

21,546

100

21,532

21,389

21,340

20,740

Rank

Player

Group

Score

Points

toshiue 2 41

Go Science

21,546

100

21,544

21,543

21,543

21,543

Rank

Player

Group

Score

Points

ZeroLeak7 70 102

Go Science

21,535

100

Enzyme 70 17

Gargleblasters

21,532

dcrwheeler 70 5

21,442

ichwilldiesennamen 27 19

Go Science

21,405

mirp 28 51

Go Science

21,356

Thu, 11/19/2020 - 02:05

Formula350 70 1803

Offline

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".

Thu, 11/19/2020 - 06:36

Bletchley Park 10 20

Offline

Joined: 05/19/2009

Groups: Contenders

objectives

@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.

Thu, 11/19/2020 - 17:25

bkoep 70 412

Offline

Joined: 11/15/2012

Groups: Foldit Staff

Whoops

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).