[jeffxtreme]

GDT_TS for AlphaFold is now comparable is at experimental levels; but that's based on the class of proteins for which we've been able to determine the 3D structure of the protein, for which there might be selection bias.

I wonder if we can determine if this extends to proteins that aren't as keen to determining their 3D structure?

For example, certain proteins are more crystallizable than others.. For these non-crystallizable proteins, I wonder if we can say that AlphaFold would generate accurate 3D models? And if possible, might there be a way to map out this uncertainty?

[deeviant]

> I wonder if we can determine if this extends to proteins that aren't as keen to determining their 3D structure?

This is already happened.

"An AlphaFold prediction helped to determine the structure of a bacterial protein that Lupas’s lab has been trying to crack for years. Lupas’s team had previously collected raw X-ray diffraction data, but transforming these Rorschach-like patterns into a structure requires some information about the shape of the protein. Tricks for getting this information, as well as other prediction tools, had failed. “The model from group 427 gave us our structure in half an hour, after we had spent a decade trying everything,” Lupas says."

From: https://www.nature.com/articles/d41586-020-03348-4

[jeffxtreme]

Agree this is great to hear, but the fact that they had X-ray diffraction data indicates this protein was indeed crystallizable no?

Though the next paragraph in the article shows that DeepMind is indeed working on mapping out reliability:

"Demis Hassabis, DeepMind’s co-founder and chief executive, says that the company plans to make AlphaFold useful so other scientists can employ it. (It previously published enough details about the first version of AlphaFold for other scientists to replicate the approach.) It can take AlphaFold days to come up with a predicted structure, which includes estimates on the reliability of different regions of the protein. “We’re just starting to understand what biologists would want,” adds Hassabis, who sees drug discovery and protein design as potential applications."

[flobosg]

> Agree this is great to hear, but the fact that they had X-ray diffraction data indicates this protein was indeed crystallizable no?

Yes. CASP uses as targets proteins with no known published structure but a solved or soon-to-be-solved one. They are then kept on hold until the end of the competition.