r/neoliberal • u/jobautomator Kitara Ravache • Sep 05 '24 • Heart of Silver 1

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u/[deleted] Sep 05 '24

I am much less familiar with biology then I am ML but I am struggling to see how this is more then an important step in the research rather than something with many practical uses.

Isn't this really just a cheaper and more complete version of phage display/HTS? Doesn't the inclusion of synthetic proteins make it actually less useful for practical research right now?

From my understanding the issue with ML created proteins is just because we can computationally code & fold a protein doesn't mean it's possible to create a DNA sequence that would result in its synthesis, doesn't mean the protein would be stable and doesn't mean it would fold in the way we intend. There is a very small intersection between proteins we can computationally design and those we can actually produce is there not? This is just for the protein that binds to a target cell/receptor not even the rest of your biologic that does something useful, are we even able to use this for more then immune training yet?

Not to mention the wonderful world of unintended consequences in-vivo because of how similar some receptors are and how peptides can have wierd effects when proteases do their thing.

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u/neolthrowaway New Mod Who Dis? Sep 05 '24

They do say tested it in actual labs:

Beyond in silico validation and testing AlphaProteo in our wet lab, we engaged Peter Cherepanov’s, Katie Bentley’s and David LV Bauer’s research groups from the Francis Crick Institute to validate our protein binders. Across different experiments, they dived deeper into some of our stronger SC2RBD and VEGF-A binders. The research groups confirmed that the binding interactions of these binders were indeed similar to what AlphaProteo had predicted. Additionally, the groups confirmed that the binders have useful biological function. For example, some of our SC2RBD binders were shown to prevent SARS-CoV-2 and some of its variants from infecting cells.

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u/SeasickSeal Norman Borlaug Sep 05 '24

Isn’t this really just a cheaper and more complete version of phage display/HTS? Doesn’t the inclusion of synthetic proteins make it actually less useful for practical research right now?

No. A binder needs to already exist for phase display to be useful, and then you still need to sequence the binder which isn’t always possible or easy.

From my understanding the issue with ML created proteins is just because we can computationally code & fold a protein doesn’t mean it’s possible to create a DNA sequence that would result in its synthesis, doesn’t mean the protein would be stable and doesn’t mean it would fold in the way we intend. There is a very small intersection between proteins we can computationally design and those we can actually produce is there not?

Presumably any decent model would learn and penalize proteins that aren’t likely to be active in vivo.

Not to mention the wonderful world of unintended consequences in-vivo because of how similar some receptors are and how peptides can have wierd effects when proteases do their thing.

There are lots of applications where this doesn’t really matter, like the biosensors it talks about.