puzzle picture
1831: Coronavirus Binder Design: Round 8
Status: Closed

Summary

Name: 1831: Coronavirus Binder Design: Round 8
Status: Closed
Created: 04/29/2020
Points: 100
Expired: 05/06/2020 - 23:00
Difficulty: Intermediate
Description: Design a binder against coronavirus! This puzzle is similar to Rounds 1 and 2 of our Coronavirus Binder Design challenge. but with tighter limits on the allowed number of segments. The starting structure has 177 segments, and players may use no more than 182 total. See the Foldit blog for tips on making a successful protein binder!

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
1Go Science14,882100
2Gargleblasters14,86985
3Team India14,86371
4Anthropic Dreams14,79260
5Contenders14,77949

Top Evolvers

RankPlayerGroupScorePoints
1ZeroLeak7 38 6 Go Science14,882100
2RockOn 41 154 Go Science14,877100
3mirp 1 3 Go Science14,87399
4Dhalion 9 93 Go Science14,87298
5Czim 14 151 Go Science14,87097

Top Soloists



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Comments

bkoep's picture
User offline. Last seen 14 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

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.

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

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 in helices.

RockOn's picture
User offline. Last seen 7 hours 5 min ago. Offline
Joined: 06/01/2011
Groups: Go Science
Tools: what tools are recommended to create a design?

If we can't drag the segments we work on and only the "Arrow" tool is available, how can we expect to design a protein that is useful? We will spend more of our time fighting the User Interface rather than the design. I watched jeff101 design videos, and they are now useless.

Is this intentional that the tool-set has been reduced?

bkoep's picture
User offline. Last seen 14 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Normal tool set

All of the regular design tools should be enabled in this puzzle. Some parts of the target protein are frozen, but you should still be able to pull on any part of the designable chain.

Which tools are inaccessible for you?

Galaxie's picture
User offline. Last seen 11 hours 46 min ago. Offline
Joined: 10/16/2011
Interaction Energy

The interaction energy bonus seems to be missing.

bkoep's picture
User offline. Last seen 14 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Oops

Good catch! That was a mistake in my comment above.

jeff101's picture
User offline. Last seen 6 hours 58 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Can we load results from previous puzzles?

If so, which previous puzzles' results are allowed here?

bkoep's picture
User offline. Last seen 14 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
No loading

No, solutions from previous puzzles are incompatible, so players may not load prior work.

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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