Using MSTA and HMMER like method to search common structure features in big database

[sevengo8378]

Thanks to FoldMason and the great work in the early stage. I have an idea. I don’t know if it is feasible or in your team’s plan?

If a database has been built using ProstT5, can we use the MSTA output (3Di format) of Foldmason and use a similar idea as hmmbuild to search for common features of multiple structures?

[milot-mirdita]

FoldMason's MSTAs are not optimized towards homology search (at least we didn't explore this, but we don't expend that globally aligned MSA are good for search purposes).

You can use Foldseek directly for profile searches. If you supply --num-iterations N (with 2-3 iterations), it will do an iterative profile search with increased sensitivity. The webserver also has a checkbox exposed that enables this mode.

[martin-steinegger]

I do think this has merits and we should provided a MSA search from FoldMason to Foldseek.

[sevengo8378]

@milot-mirdita I don't quite understand the profile searches mentioned here. Does it mean that multiple pdbs can be searched at the same time?

[sevengo8378]

thanks @martin-steinegger ，looking forward to seeing this feature soon.