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1916: MERS-CoV Binder Design: Round 4
Status: Closed

Summary

Name: 1916: MERS-CoV Binder Design: Round 4
Status: Closed
Created: 11/12/2020
Points: 0
Expired: 11/19/2020 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle was closed early due to a bug in the Contact Surface metric, and is reposted as Puzzle 1916b. Players may load solutions from this puzzle into the reposted version.

Design a binder for the viral spike of MERS-CoV! This puzzle is similar to previous, except that the SASA and SC metrics are replaced by a new Contact Surface Metric. Contact Surface captures some of the same info as both SASA and SC, and is even better at selecting successful binder designs in the lab. Contact Surface favors binders with large interfaces that closely follow the contours of the target. In this puzzle, the Metrics have a ramped bonus; as you improve DDG and Contact Surface, you will get an increasing bonus until you reach the threshold of DDG < -40 or Contact Surface > 400, and the bonus will be capped. Remember that Metrics are slow to compute and run in the background, so gameplay may be different from regular puzzles. See the blog for more info about Foldit Metrics.

MERS is a respiratory disease similar to COVID-19, and is caused by a related coronavirus. There have been several MERS outbreaks since 2012, but there is still no treatment has been developed for the disease. The MERS-CoV virus is coated with a spike protein that recognizes the human protein DPP4, which is found on the surface of lung cells. A protein that binds to the MERS-CoV spike could be used as a drug to block DPP4 recognition and slow viral infection.

In this puzzle, players are presented with the binding site of the MERS-CoV 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 MERS-CoV target, designs will need to make lots of hydrophobic contacts and satisfy any polar atoms that are buried at the interface. 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.
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Comments

bkoep's picture
User offline. Last seen 16 hours 40 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Penalizes 60 points for each polar atom that cannot make any hydrogen bonds.

Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 161, at a cost of 55 points per residue. Players may use up to 166 residues in total.

Core Existence (max +1500)
Ensures that at least 25 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.

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)
Disabled use of CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

DDG Metric (max +1000)
The predicted binding energy of your design. The goal DDG is -40.0 or less.

Contact Surface Metric (max +1000)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 400 or more.

Joined: 02/15/2018
Groups: Go Science
Whenever I try to open the

Whenever I try to open the puzzle, Foldit is closing almost immediately. Anyone having the same problem?

Joined: 09/24/2012
Groups: Go Science
me too

see feedback (I succeeded to open it the first time) Windows 10.

Joined: 05/09/2008
Groups: None
Thank you for reporting this...

We're looking into what is going on... thanks for your patience.

robgee's picture
User offline. Last seen 54 min 30 sec ago. Offline
Joined: 07/26/2013
Ditto

Same here. Opened it , it crashed, now wont open this puzzle at all. Win10

Joined: 06/06/2013
Groups: Gargleblasters
Puzzle BROKEN

I had a solid helix I was trying to move away from the target to fold. Foldit just shut and won't reopen. there is only one person on the puzzle right now. It needs a restart

grogar7's picture
User offline. Last seen 20 hours 7 min ago. Offline
Joined: 10/03/2011
same problem here

I originally opened the puzzle from an open client in which I had been playing puzzle 1914. It opened fine. Then I thought there might be an update because of the new filter. So I closed my client. When I opened a new client and tried to reopen 1916, the window briefly displays the starting position, then shuts down.

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