Comment by sabujp

Many thanks to Deepmind for releasing predicted structures of all known protein monomers. What I'd like next is for Alphafold (or some other software) to be able to show us multimeric structures based on the single monomer/subunit predictions and protein-protein interactions (i.e. docking). For example the one I helped work on back in my structural biology days was the circadian clock protein KaiC : https://www.rcsb.org/structure/2GBL, that's the "complete" hexameric structure that shows how each of the subunits pack. The prediction for the single monomer that forms a hexamer is very close to the experimental https://alphafold.ebi.ac.uk/entry/Q79PF4 and in fact shows the correct structure of AA residues 500 - 519 which we were never able to validate until 12 years later (https://www.rcsb.org/structure/5C5E) when we expressed those residues along with another protein called KaiA which we knew binds to the "top" CII terminal (AAs 497-519) of KaiC. If we would have had this data then, it would have allowed us to not only make better predictions about biological function and protein-protein interactions but would have helped better guide future experiments.

What we can do with this data now is use methods such as cryo-em to see the "big picture", i.e. multi-subunit protein-protein interactions where we can plug in the Alphafold predicted structure into the cryo-em 3d density map and get predicted angstrom level views of what's happening without necessarily having to resort to slower methods such as NMR or x-ray crystallography to elucidate macromolecular interactions.

A small gripe about the alphafold ebi website: it doesn't seem to show the known experimental structure, it just shows "Experimental structures: None available in PDB". For example the link to the alphafold structure above should link to the 2GBL, 1TF7, or any of the other kaic structures from organism PCC7942 at RCSB. This would require merging/mapping data from RCSB with EBI and at least doing some string matching, hopefully they're working on it!