Protein design, the inverse of a protein folding problem

[John Clark]

AlphaFold solved the protein folding problem some time ago and now, judging from two articles in today's issue of the journal Science, it looks like the inverse problem has also been solved, the protein design problem. If you tell a program called "ProteinMPNN" that you want a 3-D protein that has an activation site that will perform a very specific function, and has the proper scaffolding to keep that activation site stable, and is also shaped in just the right way so that it can fit into a very tight corner where it is needed like a key into a lock, then ProteinMPNN will tell you what linear sequence of amino acids will fold up into that 3-D shape. I think this is a very big deal, the implications for medicine are obvious but it also signifies a huge advance in Nanotechnology because the authors claim the 3-D shape the sequence of amino acids folds up into is within 0.06 Nanometers of the requested shape, and Nanotechnology is about placing atoms exactly where you want them to go, and enzymes are proteins and they act like little machines.  

Robust deep learning–based protein sequence design using ProteinMPNN

Hallucinating symmetric protein assemblies

John K Clark

[Brent Allsop]

There's a big difference between the way we make machines, and the way life makes machines.  Isn't all this moving us away from the current way of making machines, and now we're going to start making machines the way life does?

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[John Clark]

On Fri, Sep 16, 2022 at 1:32 PM Brent Allsop <brent....@gmail.com> wrote:

> There's a big difference between the way we make machines, and the way life makes machines.  Isn't all this moving us away from the current way of making machines, and now we're going to start making machines the way life does?

Life is a small subset of Nanotechnology in that all its machines are made with just 20 amino acids, this method is a little more generalized than that because there are hundreds of amino acids that it could use not just 20  as life does,  and it's a big step towards full scale Drexler style Nanotechnology which can make machines out of any sort of atoms or molecules not just amino acids.  

John K Clark

 

On Fri, Sep 16, 2022 at 11:02 AM John Clark <johnk...@gmail.com> wrote:

AlphaFold solved the protein folding problem some time ago and now, judging from two articles in today's issue of the journal Science, it looks like the inverse problem has also been solved, the protein design problem. If you tell a program called "ProteinMPNN" that you want a 3-D protein that has an activation site that will perform a very specific function, and has the proper scaffolding to keep that activation site stable, and is also shaped in just the right way so that it can fit into a very tight corner where it is needed like a key into a lock, then ProteinMPNN will tell you what linear sequence of amino acids will fold up into that 3-D shape. I think this is a very big deal, the implications for medicine are obvious but it also signifies a huge advance in Nanotechnology because the authors claim the 3-D shape the sequence of amino acids folds up into is within 0.06 Nanometers of the requested shape, and Nanotechnology is about placing atoms exactly where you want them to go, and enzymes are proteins and they act like little machines.  

Robust deep learning–based protein sequence design using ProteinMPNN

Hallucinating symmetric protein assemblies

John K Clark

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