How to compare multiple protein structures with TM-align

[xubai]

Dear Zhang Lab teams,

I'm trying to find the human homologue of a protein by structural similarity. Firstly, I used Alphafold3 to get information about its structure (.PDB), now I wonder how to find a human protein with high similarity to it? Do I need to download the structure file for all homo sapiens proteins in the PDB database?

Thank you! I am looking for you reply.

[zcx@umich.edu]

AlphaFold structures of all human proteins can be downloaded via the alphafold database
https://ftp.ebi.ac.uk/pub/databases/alp ... MAN_v4.tar
You can then perform pairwise TM-align alignments. You probably would want to use the "-fast" option of the TM-align (C++ version only) or US-align, as there are ~20000 alignments to perform.