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1849: Coronavirus Binder Design: Round 11
Status: Closed

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bkoep's picture
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Joined: 11/15/2012
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Objectives

Buried Unsats (max +500 +0)
Detects polar atoms that cannot make hydrogen bonds. Note that the frozen target includes 8 buried unsats that may be impossible for players to satisfy. This Objective awards no bonus or penalty.

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 and helices.

Xartos's picture
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Buried Unsats (max +500)

???

I didnt started the Puzzle yet but description tells different.

bkoep's picture
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Joined: 11/15/2012
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You're right

Fixed!

HMK's picture
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Available surface on the the rbd?

Which is the available surface on the frozen part of the puzzle?
As far as I understood, mainly the nick (notch?) of the "saddle" of the frozen part in this puzzle is accessible for the designed protein.
Do the flanks of this "saddle" also belong to the accessible parts of the receptor-binding-domain or are they blocked by other structures?
(e.g. as the spike protein is a trimer, these parts may be covered by another chain of the trimer.)

bkoep's picture
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Good question!

Only the flexible orange/blue sidechains should be targeted. This includes some of the flanking regions of around the "saddle." These are the residues that the spike uses to recognize the human ACE2 receptor, and we want to block those residues with our designed binder.

Other parts of the target have frozen gray sidechains. These should be avoided because they are not involved in ACE2 recognition (so we don't need to target them), or because they would be blocked by other parts of the spike protein.

agcohn821's picture
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Question

Hey HMK! Thank you so much for your question--I will pass it along to the team.

LociOiling's picture
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see also:

Here's a blog comment discussing a couple of ways to get a better picture of the binding site: https://fold.it/portal/node/2008989#comment-41872

HMK's picture
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Thank you

Thanks to all of you for your helpful answers.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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