Starting protein in Binder puzzle

Case number:699969-2012101
Opened by:nspc
Opened on:Thursday, September 23, 2021 - 21:28
Last modified:Tuesday, September 28, 2021 - 19:42

In design puzzles maybe we can add a very stable tripple helix as starting protein (or other proteins when we use "reset puzzle").

Maybe that would allow us to create more designs that folding would be easier to predict in its lab version.

(Thu, 09/23/2021 - 21:28  |  2 comments)

bkoep's picture
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Yes, that might make these puzzles easier, but we are afraid this could bias players toward designs that look like the starting structures. This would jeopardize the ultimate diversity of solutions, which is one of the main benefits of the "Foldit approach."

In fact, we have computer algorithms that are very good at making lots of variations from a starting scaffold. For many protein design problems, this is part of the standard approach: a scientist starts with a set of stable scaffolds and then uses a supercomputer to make thousands and thousands of variations on that scaffold. Then they hunt through all of these variations for ones that look best suited for their particular problem (binding a protein target, binding a small molecule, etc.). In a lot of cases this approach is very effective, but in other cases the scientist is limited by their starting scaffolds. Maybe their problem can't be solved by a simple variation on a three-helix bundle.

That's where Foldit approach comes in. Rather than "mindlessly" creating thousands and thousands of variations, we hope Foldit players might be able to intelligently craft an appropriate protein design from the ground up. Even if your Foldit strategy is to start by making a 3-helix bundle, your Foldit-created bundle will probably be unlike the computer-generated scaffolds that the scientists have. The result is that the Foldit solutions from any puzzle are diverse from the computer-generated solutions in the lab. We think this diversity is one of the greatest strengths of Foldit, so we want to be careful about adding tools or features that might inadvertently reduce the diversity of Foldit solutions.

nspc's picture
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Thanks for answer. I understand more ^^.


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