puzzle picture
1874: Coronavirus Binder Design: Round 15
Status: Closed

Summary

Name: 1874: Coronavirus Binder Design: Round 15
Status: Closed
Created: 08/06/2020
Points: 100
Expired: 08/13/2020 - 23:00
Difficulty: Intermediate
Description: Design a binder against coronavirus! We'd like players to keep focusing on making closely packed interfaces with no extra BUNS. This puzzle prohibits SER and THR in helices, which may make it harder to satisfy BUNS, but should help the helices to fold correctly. Remember, if your designed protein creates Buried Unsats, then it will be less likely to fold and bind to the coronavirus target. (Note that this target protein includes 8 buried unsats that players may be unable to fix.) See the blog for more details about buried unsats, and for helpful tips to make a successful protein binder! Players may not load solutions from previous puzzles.

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 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 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
1Gargleblasters14,917100
2Go Science14,81877
3Anthropic Dreams14,78958
4Contenders14,63843
5Beta Folders14,57131

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
1mirp 1 1 Go Science14,797100
2phi16 8 23 Anthropic Dreams14,76898
3ZeroLeak7 47 16 Go Science14,73995
4malphis 113 8  14,73792
5Joanna_H 35 13 Gargleblasters14,72790


Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 20 hours 6 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +20)
Penalizes 60 points for each polar atom that cannot make any hydrogen bonds. Note that the frozen target includes 8 buried unsats that may be impossible for players to satisfy.

Residue Count (max +275)
Penalizes extra residues inserted beyond the 177, at a cost of 55 points per residue. Players may use up to 182 residues in total.

Core Existence (max +2400)
Ensures that at least 25 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, SER, THR in helices.

bkoep's picture
User offline. Last seen 20 hours 6 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Devprev puzzle

Devprev users can try loading your solutions into the new devprev puzzle to check the DDG, SASA, and Shape Complementarity metrics of your binder.

Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Other Games: Mozak
Search
Only search fold.it
Recommend Foldit
User login
Topics
Top New Users
Sitemap

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