Structural alignment of protein

Question

[Sadik Muzemil]

Hi all,

I am newbie to structural alignment. Is there a way to do structural comparison of a query predicted structure against protein structures in the database say AlphaFold predicted protein structure or other?

The protein I am working on does show limited sequences homology with other proteins in closely related species but AlphaFold2 (AF) prediction resulted high-confidence prediction (plddt > 80%).

The aim to get an idea about evolutionary role of this protein and thought that structural comparison with other predicted protein structures might help. The challenge would be how one select the reference protein to compare or whether there is a way do to global structural comparison - I have no idea:)

Suggestions on how it can be dealt with would be highly appreciated.

Answer 1

[Mensur Dlakic]

Foldseek can search many databases of structures, including those made by AlphaFold2.

https://search.foldseek.com/search

Foldmason can align multiple protein structures.

https://search.foldseek.com/foldmason

[Sadik Muzemil]

Thanks a lot Mensur Dlakic exactly what I am looking for. I will look into the paper for details.