Curious since AlphaFold got released: have classical molecular dynamics sims in this area become obsolete, at least for protein folding? How does the research coming out of venues like DESRES compare? Are they working on more specific problems in the same area or are they in a different business altogether?

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the__alchemist 8 hours ago | parent | next [-]

No. AlphaFold doesn't do dynamics; it does end-state snapshots only. It does not do anything about the motion of the atoms, which is the core functionality of MD.

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tripplyons 8 hours ago | parent | prev | next [-]

I was curious about what was released, and the parameters for AlphaFold V3 are only given to certain groups for non-commercial use: https://github.com/google-deepmind/alphafold3?tab=readme-ov-...

However, it seems like anyone can download the parameters for AlphaFold V2: https://github.com/google-deepmind/alphafold?tab=readme-ov-f...

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dekhn 7 hours ago | parent | prev [-]

MD was never really a viable way to do structure prediction, so it didn't become obsolete with AlphaFold. Instead, MD is more useful for studying the physical process of protein folding (before the protein folds to its final structure, as well as once it has reached its final structure and sort of jiggles and wiggles around that).

	▲	cowsandmilk 5 hours ago \| parent [-]
		MD simulations typically aren’t run for time scales that tell you anything about the folding process. Most people are looking at motion after the protein has folded.