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1828b: Coronavirus Anti-inflammatory Design: Round 2
Status: Closed

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bkoep's picture
User offline. Last seen 16 hours 58 min 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.

jeff101's picture
User offline. Last seen 23 hours 9 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Ideal Loops Bonus

I think recipes would work better on puzzles like
this if the Ideal Loops Bonus depended on the total #
of residues in non-ideal loops rather than the # of
non-ideal loops. This way, shorter non-ideal loops would
score better than longer ones, and if you changed a
14-residue non-ideal loop into 2 non-ideal loops each
with length 5, your score would improve.

See https://fold.it/portal/node/2005262#comment-41271
for more details.

agcohn821's picture
User offline. Last seen 9 hours 16 min ago. Offline
Joined: 11/05/2019
Groups: Foldit Staff
Thank you!

Hey Jeff101!

Thank you so much for the suggestion--I have passed it along.

Joined: 04/25/2020
Groups: Go Science
Multi purpose protein?

Is there value in a anti-inflammatory protein also capable of bonding to the covid spike? Obviously bonding to IL6R would take priority, but every protein has multiple angles and there may be a non intrusive way to allow one side to bond to part of the spike.

bkoep's picture
User offline. Last seen 16 hours 58 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Probably not

That's an interesting idea! But, in general, we prefer to have drugs that interact each with a single target. This gives doctors greater control over the treatment program. I think this would outweigh any advantages to having two functions on the same molecule (in this case, at least).

Ideally, we'd like to have one drug that targets the CoV spike, and one that targets IL6R. If a doctor decides both drugs are necessary, then they can both be administered (and hopefully there are no complex drug interactions). If the same drug targets both IL6R and CoV spike, then there is no way for a doctor to treat one without affecting the other.

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