• ranzispa@mander.xyzOPEnglish
      22·
      3 months ago

      Not solved, no. Definitely much much better than before. The difference AlphaFold made is significant: we’re talking about getting a decent model in a couple minutes using a PC compared to several months of calculations before.

      However we still need experimental data: in many occasions AlphaFold gives an incorrect model. With some experimental data that model can be improved, but we still have no reliable way to know what the structure of a protein is starting from the amino acidic sequence without extensive experimentation.

      That’s the big promise of quantum computers, there are however two major problems in my opinion:

      1. There’s still no theoretical framework which explains how once we have a quantum computer we may tackle protein folding
      2. Plenty quantum computing companies closed shortly after AlphaFold was published since they lost all funding because protein folding was “solved”
          • ranzispa@mander.xyzOPEnglish
            4·
            3 months ago

            I doubt there is a comparable correctness metric between LLMs and protein structure prediction models.

            You can measure how many times they correctly predict a thing, but results will greatly change according to what your objective is. Those are only comparable when you’re trying to predict the same thing.

            As such my reply would be: sometimes more incorrect sometimes more correct. However, in general, a mishandled incorrect protein structure prediction is way more expensive than an LLM hallucination.

      • ComradeSharkfucker@lemmy.mlEnglish
        5·
        3 months ago

        A reliable way to simulate any kind of protein fold. As long as you have a method you could hypothetically “solve” the issue

      • SaveTheTuaHawk@lemmy.caEnglish
        3·
        3 months ago

        There actually aren’t. However, some of the most interesting proteins have no structure at all.

        • ranzispa@mander.xyzOPEnglish
          2·
          3 months ago

          The interesting part would be to a reliable and computationally accessible way to handle disordered proteins. Seeing how they can move could be quite revolutionary.

          I had to work on some disordered proteins and you’re pretty much just guessing, plausibly you’re better off going to a casino blindfolded and play blackjack.