puzzle picture
1912: Designable Linker: Coronavirus Spike Binder
Status: Closed

Summary

Name: 1912: Designable Linker: Coronavirus Spike Binder
Status: Closed
Created: 11/03/2020
Points: 0
Expired: 11/11/2020 - 23:00
Difficulty: Intermediate
Description: Note: Due to an error with the BUNS Objective, this puzzle was closed early and reposted as Puzzle 1912b.

This is the first 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 20 angstroms of the termini of the binders, so you know what regions your binder has to avoid to prevent clashing.

Currently everything is frozen except for the linker and a portion of the helix on each binder. These residues are designable, but only residues on the linker itself can be added and deleted. The two binder domains are held in place with strong constraints.

We have included a few objectives to help players generate well-folded designs. This puzzle uses the Buried Unsats Filter only on the linker to make sure buried polar atoms are making hydrogen bonds. It is a difficult problem to design a linker that can hold the binders in place. This type of puzzle is new for Foldit, and we are excited to see what players come up with!
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neilpg628's picture
User offline. Last seen 5 hours 46 min ago. Offline
Joined: 08/01/2019
Groups: Foldit Staff
Objectives

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.

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -60 points per atom.

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

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

Joanna_H's picture
User offline. Last seen 2 days 7 hours ago. Offline
Joined: 12/29/2010
Groups: Gargleblasters
Buried Unsats

Is there a problem with BUNS??? The more you have the higher your score.

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