Re:Ask HN: Breakthrough in Protein Folding
by Rochus on Sunday February 02, 2025 @08:40AM
(#42908576)
Sounds interesting. Since there is already Alphafold, I would assume that your solution concentrates on Alphafold's main weakness: the restriction on cristal structures and steady state, i.e. a single structure snapshot in an unrealistic environment. I would assume that an MD based solution like yours would be able to simulate the movement of structure parts and its interaction with a specific environment. The major challenge of MD so far (as far as I remember) was the computability of decently large proteins in reasonable time. Can you please explain how your solution improves on this? Do you have publications?
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Re:Ask HN: Breakthrough in Protein Folding
by samsamlh on Sunday February 02, 2025 @09:17AM
(#42908760)
I don’t have publications, I was trying to solve the TSP problem and found a fundamental building block of reality.
It applies to many fields.
Here is the method to apply in 3D coordinates of the protein, everything else aligns naturally
I did this post https://www.reddit.com/r/numbertheory/s/UBrRPeIGrx
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Re:Ask HN: Breakthrough in Protein Folding
by Rochus on Sunday February 02, 2025 @09:28AM
(#42908824)
What is your qualification in molecular biology and/or biophysics?
Re:Ask HN: Breakthrough in Protein Folding
by samsamlh on Sunday February 02, 2025 @09:33AM
(#42908857)
High School, I inferred everything with the maths behind the transforms. AI helped a lot. Do you successfully used the method?
Re:Ask HN: Breakthrough in Protein Folding
by Rochus on Sunday February 02, 2025 @09:39AM
(#42908903)
Well, then I recommend that you invest a few more years in university level studies to understand the subject matter, and then again try to provide an efficient solution to the protein folding problem using MD. Good luck.
Re:Ask HN: Breakthrough in Protein Folding
by samsamlh on Sunday February 02, 2025 @11:11AM
(#42909513)
Try to understand the maths, apply the circle / sphere transform and you’ll see that naturally it converges to a stable state. MD is the hard way, spherical transform is the easy way (nature uses it)
My theory on maths shows that any shape can have its points on a circle edge and midpoints on that same circle edge morphing showing all possible paths through radius scaling (P=C). It’s all about constraints.
Transforming the protein through 3D coordinates aligns all forces so it is fundamentally different than MD, it’s a geometric solver, so it is super fast!