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1918: Designable Linker: Coronavirus Spike Binder
Status: Closed

Summary

Name: 1918: Designable Linker: Coronavirus Spike Binder
Status: Closed
Created: 11/17/2020
Points: 0
Expired: 11/25/2020 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle was closed early due to some scoring problems, and has been reposted as Puzzle 1918b. Players may not load solutions into the reposted puzzle.

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.

Currently everything is frozen except for the linker, and those residues are completely designable. The two binder domains are held in place with strong constraints.

We have included a few objectives to help players generate well-folded designs. We have added the Ideal Loops Objective as another difference from puzzle 2. 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 15 hours 13 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.

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.

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.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons