puzzle picture
1828: Coronavirus Anti-inflammatory Design: Round 2
Status: Closed

Evolvers

RankPlayerGroupScorePoints
26jausmh 17 29 Marvin's bunch10,2770


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bkoep's picture
User offline. Last seen 2 days 3 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 152, at a cost of 55 points per residue. Players may use up to 157 residues in total.

Core Existence (max +1000)
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.

Joined: 04/23/2020
Groups: None
idk

idk

Joined: 09/24/2012
Groups: Go Science
Unideal locked loops?

Locked 116 is abego green which shows no candidate ideal loop in brueprint.
Locked 127-1238 are abego red but the ideal SS function keep them as a(non ideal) loop, which makes it difficult to build an ideal loop there.
7 invalid residues in the locked protein.

Joined: 12/07/2007
Groups: Contenders
There's a problem with the

There's a problem with the Ideal Loop filter here: no matter what I do I can't get ideal loops at the ends of the frozen helix and so end up with two non-ideal loops: it appears that others are having the same issue.

Susume's picture
User offline. Last seen 15 hours 12 min ago. Offline
Joined: 10/02/2011
Not possible to get ideal loops there

At the beginning of the locked helix, there is one locked residue in the green abego area. We don't have any ideal loops that have a green right before a helix, so no one will be able to get an ideal loop there. At the other end, there are two loop segments that are abego-red, but the helix backbone bonds are disrupted there, so they can't be counted as part of the good helix. We also don't have any ideal loops after a helix that start with two reds, so no one will be able to get an ideal loop there.
The "good" new is it's an even playing field - no one will be able to get the bonus for those two loops. The bad news is it's very frustrating and lots of players will spend lots of time trying in vain to fix it.

Susume's picture
User offline. Last seen 15 hours 12 min ago. Offline
Joined: 10/02/2011
Peptide bond 128-129 is bad

I turned on stick view and all the show options needed to see the O, N, and bondable hydrogen atoms. The peptide bond between 128 and 129 is bad - almost but not quite cis. The H on 129's N is on the same side of the backbone as the O at the end of 128. That makes it impossible to extend the helix - it makes a horrible U-turn there if tou try it. It is possible with aggressive banding and cutpoints to get it closer to trans, but not all the way to 180*. My guess is everybody's protein is going to be unrealistic at that spot.

bkoep's picture
User offline. Last seen 2 days 3 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good catch!

We've closed this puzzle and reposted it as Puzzle 1828b. In the reposted puzzle, the problem residues at both ends of the helix have been unlocked.

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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, Boehringer Ingelheim, RosettaCommons