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It's kind of surprising that AlphaFold has some success with random sequences of amino acids: > "Baker’s team gets AlphaFold and RoseTTAFold to “hallucinate” n
by photochemsyn 5y ago
It's kind of surprising that AlphaFold has some success with random sequences of amino acids:
> "Baker’s team gets AlphaFold and RoseTTAFold to “hallucinate” new proteins. The researchers have altered the AI code so that, given random sequences of amino acids, the software will optimize them until they resemble something that the neural networks recognize as a protein. In December 2021, Baker and his colleagues reported expressing 129 of these hallucinated proteins in bacteria, and found that about one-fifth of them folded into something resembling their predicted shape."
20% is not that great but it has potential. One long-standing goal is the de novo design of protein-based industrial catalysts for specific chemical transformations. Proteins from bacteria that live in boiling sulfur vents etc. have been used to some extent, but the idea is that similar proteins could be designed for a much wider variety of industrial processes. As the article notes, specificity remains a challenge (and designed proteins don't approach the efficiency of the evolutionary selected proteins), but it still seems promising.
P.S. I'm a bit more skeptical about the drug-design programs. It's not so much that novel drugs can't be designed that bind to the desired targets, it's that they might bind to a whole lot of undesired targets as well, leading to nasty side effects. Now if you could screen against the whole proteome, perhaps.
- flobosg 5y ago> 20% is not that great but it has potential. 20% success rate is in line with other protein design methods, though.
- gfodor 5y agoI'd imagine the success rate isn't apples to apples - the real measure is "time, energy, and manpower expenditure needed per generated protein"
- flobosg 5y agoBoth measures can be quite similar. Most protein designs can be screened in parallel for solubility and successful designs can be further engineered and tested in a high-throughput manner.
- jimmySixDOF 5y agoTalking about higher level applications, BBC Science in Action [1] interviewed Prof John McGeehan of the Centre for Enzyme Innovation at Portsmouth University working on Bacteria breaking down Plastic in landfills. He explained his workflow of maybe selecting one candidate occasionally out of many due to the cost/time involved & how DeepMind gave him more results in one weekend that he had expected to see over his entire career. [1] https://www.bbc.co.uk/sounds/play/w3ct1l3y https://www.bbc.co.uk/sounds/play/w3ct1l3y
- Teever 5y ago> and designed proteins don't approach the efficiency of the evolutionary selected proteins This sounds interesting. Can you talk more about this? Efficiency in what sense, energy efficiency in the actual protein assembly in biological systems, or efficiency in actual performance of the protein while it's functioning in a biological system?
- flobosg 5y agoHe’s probably referring to the catalytic efficiency of designed enzymes, so your second option.