3 ms·
now that we have this inevitable discussion venue after everyone has digested the PR (and some of the people her might have even had a chance to ask some questi
by fock 6y ago
now that we have this inevitable discussion venue after everyone has digested the PR (and some of the people her might have even had a chance to ask some questions to deepmind) some remarks (questions - if anyone from the team is here):
- I thought that open code was becoming the standard and also being pushed by Google? But apparently this does not apply to deepmind, because of $$$s? For the original Alphafold (which actually was 3 models) no code is available except, where it had to be (their nature publication on one of the three models used in the competition).
- why did they not participate with all the available proteins? I guess it's some loophole in the rules, to allow for greater "improvements" even when models are not super general, but from a naive scientific view that is absolutely stupid.
- maybe they went fully generative this time, but in CASP13, 2/3 of their models were just blackbox-predictors, which they optimized with simulated annealing. Given that the configurational sample space for the protein is huge, doing that seems still rather costly. I wonder how the actual spectra fitting works and compares to that and why experimentalists could not go this route as well? (just do simulated annealing, until the spectrum fits).
- they already trained on all known proteins, yet with some they are still far off. Seems like it's not solved really, though results are certainly impressive and it could be a great tool for any person interested in frozen protein structures.