Running foldmason with 3Di sequence input, not PDB file

[iwilkie]

Hi!

First of all thank you for all the tools you've been working on, they're super helpful!

I'm trying to generate a MSA using the 3Di, but haven't found a tool for that yet which doesn't require a structure file input. I'm comparing many structures, and am hoping to skip a full structure prediction, so was thinking that aligning the 3Di sequence might be a workaround to see conservation at the structural level.

Is it possible to run foldmason without PDB inputs, instead using the 3Di sequence (or the amino acid sequences)? I realise then you wouldn't get the structure part in the output, but it would still provide the MSA.

Thanks in advance,
Isa

[milot-mirdita]

Foldmason currently needs full structures, as it uses the backbone coordinates to score the MSA. We are exploring using ProstT5 with Foldmason, but that is still very early stages and will need more time.

[iwilkie]

Thanks for letting me know!