puzzle picture
1805b: Coronavirus Spike Protein Binder Design
Status: Closed

Summary

Name: 1805b: Coronavirus Spike Protein Binder Design
Status: Closed
Created: 02/27/2020
Points: 100
Expired: 03/05/2020 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle replaces Puzzle 1805, in which some tools were unintentionally disabled. Players may load in solutions from Puzzle 1805.

Design a binder against coronavirus! 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 sidechains at the binding site, where the spike protein normally interacts with the human receptor protein. Players can design a new protein that binds to these sidechains, blocking interactions with the human receptor. In order to bind the coronavirus target, designs will need to make lots of contacts and H-bonds with the spike protein at this 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
1Go Science16,812100
2Gargleblasters16,74884
3Anthropic Dreams16,56170
4Beta Folders16,53457
5Contenders16,50847

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
1Bruno Kestemont 2 4 Go Science16,782100
2ZeroLeak7 38 6 Go Science16,756100
3actiasluna 23 16 Gargleblasters16,748100
4Glen B 172 81  16,66899
5johnmitch 172 14  16,55299


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Comments

bkoep's picture
User offline. Last seen 2 hours 23 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.

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
7 invalid residues in Corona

For info: we are penalized for 7 invalid residues in the Corina protein. This cannot be changed. The SS design max is 150 (not 500).

Maximum total bonus is 3600 (not 3950)

Maximum number of additional segments is 10, with a maximum total bonus of 3050.

LociOiling's picture
User offline. Last seen 4 hours 36 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
chat and wiki

There's a coronavirus chat on 29 February in US timezones. The chat is arranged by joshmiller, and is happening on the new Foldit Discord server. This is a short notice, impromptu chat to discuss a hot new puzzle. Worst case, it's an opportunity to see what Discord offers.

You'll need a free Discord account to participate, and the chat happens 29 February at noon Eastern standard time, 09:00 Pacific standard time, or 1700 UTC/GMT/Zulu on the Foldit server.

There's also a Coronavirus Spike Protein page on the Foldit wiki, still a work in progress.

jeff101's picture
User offline. Last seen 2 hours 52 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Please record and post the Coronavirus Chat

I won't be able to participate in the Coronavirus Chat on Feb 29. Would it be possible for you to record it and post it online somewhere so I can watch it later? Video, audio, or an all-text transcript would be useful.

Joined: 06/06/2013
Groups: Gargleblasters
record of chat

Like Jeff, I was out of computer reach for Corona chat. Can we get a link for those of us with time management challenges? It would be handy, and we don't say much ;)

Joined: 02/15/2018
Groups: Go Science
This is an exciting puzzle.

This is an exciting puzzle. Thanks for allowing us to design proteins targeting the spike protein.
Is it possible for us to share more than 5 designs with the scientist (For instance 8 or 10 designs) ?

bkoep's picture
User offline. Last seen 2 hours 23 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Yes!

Please Share with Scientists as many times as you would like for this puzzle! We will definitely take a look!

Joined: 03/03/2020
Groups: None
Can I participate from Android phone

Is this playable on Android phones?

LociOiling's picture
User offline. Last seen 4 hours 36 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Foldit runs on Windows, Mac OS, and Linux

Foldit uses lots of computing power, so it's not available on mobile platforms at present.

Joined: 06/02/2020
Groups: None
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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