Looking at the supplementary material (section 2.5.4) for the AlphaFold 3 paper it reads to me like they still use NMR structures for training, but not for evaluating performance of the model.
I think it's implicit in their description of filtering the training set, where they say they only include structures with resolution of 9A or less. NMR structures don't really have a resolution, that's more specific to crystallography. However, I can't actually verify that no NMR structures were included without directly inspecting their list of selected structures.
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.
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).
> 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.
