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1912b: Designable Linker: Coronavirus Spike Binder
Status: Closed


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bkoep's picture
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Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 205, at a cost of 55 points per residue. Players may use up to 215 residues in total.

Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -60 points per atom.

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

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.

HuubR's picture
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Can someone please explain this?

This is an exciting new type of puzzle, and I was very motivated to give it my best shot, but then I ran into something I do not understand.

The puzzle description above says that we have "two of the best-known designed binders", and I can understand that these are fixed in space with strong constraints (the thin red lines, when you move a part out of position). And the description of the first image in Coronavirus Designable Linker Puzzles says "The binders have been [...] augmented with helices to bring their termini closer together". As I see it, those are the parts of the helices that are all Valine (residues 76-92 and 131-142). These are supposed to be designable. Why, then, are these also constrained in space? If I want to redesign part of these helices, I can mutate, but I cannot bend the backbone, not even a little bit, without a huge penalty in points. Let alone replacing part of these helices with another structure.

In my mind, this will not help to get diverse and creative solutions!

It could well be that I'm just missing something here, so if anyone can explain this to me, that would be greatly appreciated.

neilpg628's picture
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Yes, for that puzzle the helices were mutable but not deletable or designable. That is now changed for the newer Designable Linker Puzzle being released today.

APPAAP's picture
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I cannot best advise to the above questions.

Furthermore is there anyone who knows how to resolve a problem with an information pin placed at segment 132 (at beginning of puzzle this is Glutamate)and segmented one this makes also segment 131 to score poor (no good state) . The information pin says that we can use the idealize tool but if you try to use it a lot of bad thing's happen and all the structure become a mesh with constrained red lines!!

I experience also that in some puzzles and probable this one a)design freedom is relative, well notice that we do not have the SARS CoV-2 surounding structure b)processing power is important to some puzzles to achieve higher energy scores because it clearly relates to effective combinations except if you have a very good idea about the solution c) the efficiency of recipes (lua algorithm) is important. In conclusion is not only human creativity (only playing) but all above mentioned which contribute to the final result as well knowing the very details of using this software (playing skills).

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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