Find protein structure from gene id?

[cmdcolin]

I was wondering if it was possible to use gget to lookup, given a gene/transcript id, the 3d protein structure pdb file or mmcif from perhaps alphafold db or elsewhere. I was hoping to be able to do this without de novo alphafold prediction if a precomputed structure could be found, and fallback to de novo prediction if precomputed was not found. I looked at foldseek as another option but hadn't yet figured it out

[lauraluebbert]

Hi Colin, I'm not sure if this is what you were looking for, but I created this Colab notebook showing how you can use some of the gget modules to approach this problem.

[cmdcolin]

wow that is a great demo, thank you! all the steps from looking up whether the actual queried id has a pdb id, to finding related proteins, to performing de novo alphafold. I may need to even think about moving some of my own work into colab