Integrating Alphafold structures

[katewarner]

Explore integrating Alphafold cross-referencing and 3D structures of proteins not in PDB

[Luke-Johnson-5]

Alphafold 3 server is very interesting and maybe something for the future. https://golgi.sandbox.google.com/

However, at this time it is still in the beta and alphafold 3 is not open source... with a current limit of 20 queries per day.

[katewarner]

@Luke-Johnson-5 it does look interesting, and I can see it has a glycan example! - https://golgi.sandbox.google.com/example/examplefold_pdb_7bbv

Thanks for the heads up. Hopefully they'll make it open source soon so we can use it.

[jeet-vora]

@pkay47

We will need your help in integrating Alphafold structures. Can you try to find answers to the questions. Kate and I will be working with you.

• [ ] What files does UniProt import to show Alphafold structures - PDB or mmCIF?
• [ ] Are there any cases where there is more than one predicted structure?
• [ ] Are Alphafold structures present for all glygen organisms

[pkay47]

@jeet-vora Uniprot uses alphafold api https://alphafold.ebi.ac.uk/api/prediction/ & uses the cif url in the response to display structures.

eg: https://alphafold.ebi.ac.uk/api/prediction/P05067 ; Response also has info like version, pdburl for structure in pdb format, etc

AlphaFoldDB xrefs is available for 9 organisms. No xrefs for viruses.