AlphaFold 3 predicts the structure and interactions of all of life's molecules

Re:AlphaFold 3 predicts the structure and interactions of al... by fabian2k on Wednesday May 08, 2024 @12:15PM (#40299790)

I think it is very plausible that they don't use NMR structures here, but I was looking for a specific statement on it in the paper. I think your guess is plausible, but I don't think the paper is clear enough here to be sure about this interpretation.

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Re:AlphaFold 3 predicts the structure and interactions of al... by dekhn on Wednesday May 08, 2024 @12:18PM (#40299820)

Yes, thanks for calling that out. In verifying my statement I actually was confused because you can see they filter NMR out of the eval set (saying so explicitly) but don't say that in the test set section (IMHO they should be required to publish the actual selection script so we can inspect the results).

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Re:AlphaFold 3 predicts the structure and interactions of al... by fabian2k on Wednesday May 08, 2024 @12:25PM (#40299919)

Hmm, in the earlier AlphaFold 2 paper they state:

> Input mmCIFs are restricted to have resolution less than 9 Å. This is not a very restrictive filter and only removes around 0.2% of structures

NMR structures are more than 0.2% so that doesn't fit to the assumption that they implicitly remove NMR structures here. But if I filter by resolution on the PDB homepage it does remove essentially all NMR structures. I'm really not sure what to think here, the description seems too soft to know what they did exactly.

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