puzzle picture
1818: Coronavirus Binder Design: Round 5
Status: Closed

Summary

Name: 1818: Coronavirus Binder Design: Round 5
Status: Closed
Created: 03/27/2020
Points: 100
Expired: 04/03/2020 - 23:00
Difficulty: Intermediate
Description: Design a binder against coronavirus! We're challenging players to design an antiviral protein that could bind to the 2019 coronavirus spike protein and disrupt viral infection. The starting structure is a solution designed by spvincent in our previous Round 2 puzzle. This solution makes an excellent interface with the target, but we're concerned that the binder may not fold properly. Our predictions suggest that the two sheets in this solution will not fold up as designed. We're asking Foldit players to try and improve this design so that it folds up correctly and can bind to the target! Players also have freedom to redesign an entirely new solution from scratch.

In late 2019, a new highly-infections virus emerged out of Wuhan, China. This virus belongs to the coronavirus family, and is similar to the virus that caused the SARS epidemic in 2002. Coronaviruses display a "spike" protein on their surface, which binds tightly to a receptor protein found on the surface of human cells. Once the coronavirus spike binds to the human receptor, the virus can infect the human cell and replicate. In recent weeks, researchers have determined the structure of the 2019 coronavirus spike protein and how it binds to human receptors. If we can design a protein that binds to this coronavirus spike protein, it could be used to block the interaction with human cells and halt infection!

In this puzzle, players are presented with the binding site of the coronavirus spike protein. The backbone and most of the sidechains are completely frozen, except for flexible sidechains at the binding site, where the spike normally interacts with the human receptor. Players can design a new protein that binds to these sidechains, blocking interactions with the human receptor. Successful binder designs will need to make lots of hydrophobic contacts and H-bonds with the flexible sidechains at the binding site. But designs will also need to have lots of secondary structure (helices or sheets) and a large core, so that they fold up correctly! See the puzzle comments for Objective details.
Categories: Design, Overall

Top Groups

RankGroupScorePoints
1Contenders16,420100
2Go Science16,39088
3Anthropic Dreams16,37477
4Gargleblasters16,36167
5Hold My Beer16,33758

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Comments

bkoep's picture
User offline. Last seen 3 hours 51 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 192, at a cost of 55 points per residue. Players may use up to 202 residues in total.

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

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

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.

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

Joined: 09/24/2012
Groups: Go Science
do you expect

that we try to keep the structure of the face binding to the virus ? (then bot mutating the binding without burials of the helices). ?

bkoep's picture
User offline. Last seen 3 hours 51 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Up to you!

We think the starting interface looks pretty good, so it might be okay to keep the binding face the same and focus on refolding the sheets.

However, if you think you can improve the binding interface, go for it!

Joined: 03/30/2020
Groups: None
hüpfen

ich finde es ist nicht nur ein Spiel es hilft auch den Wissenschaftlern,rinenn das corona Virus zu bremsen.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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