New tool for the Lab: "Bonding forces" slider

  • 6
  • Idea
  • Updated 7 years ago
Add a slider "Bonding forces" to the lab's design interface.
With this slider you could steplessly decrease the bonding forces between nucleotides from 100% (default value) down to 50%.
This could be a way to find potentially weak spots in your design.
Of course you'd have to use as less G-C pairs as possible when you design with decreased bonding forces, otherwise you'd end up with a christmas tree.

Alternatively the slider could decrease only the forces between pairs in the target shape whereas forces between unintentional pairs would remain constant.
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Madde

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  • happy

Posted 9 years ago

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dimension9

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Wow, Madde! Great idea! As you move the slider, the weakest bonds would begin to separate - enabling you to find weaknesses where you might not have expected them - and therefore, also enabling you to try out different configurations for minimizing weaknesses in critical locations. I like this idea a lot.

-d9
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Matt Baumgartner [mpb21], Alum

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Yes this sounds like an awesome idea
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jandersonlee

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kind of like turning up the heat.
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Edward Lane

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consider also turning up the bonding forces to 200% - you might get mispairs happening easier ?
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yoffset

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Good thing I searched first. This is my idea too. Actually, I was thinking from 0% up. That way we could see which G C attracted first, second, etc. from Natural. Slow motion would be helpful too.
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Edward Lane

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Was just thinking about how this could be used to compare the lab submissions with the lab results. If the continuous colour value is correct, and the estimated shape is accurate (or close to accurate) then sliding the bond strengths ever so slightly so that the submitted sequence in natural mode goes to the estimated shape should give a better indication of what the bond strength in the eterna model should be. If it's consistent over all lab results. Or (I think) if it's inconsistent it should show where the estimated shapes are in error.
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jnicol, Player developer

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I have been talking about a tool that could help show where the instability in a design lies. If a tool could show how much difference in energy between bonds would result in an alternate shape, then this would be an invaluable tool to use in the switch lab designs. Thanks to Mat for listening to my rants and directing me to this thread, where I see this idea has been around for over a year! This is a great idea and it is time for it to be implemented. With the success of Summers Back in the current lab which uses a variation of this idea, I think there is enough evidence to merit the development of this tool. Thanks for listening to my rants again :)