Using structure prediction approaches to predict interaction between two proteins

Question

[Daniel]

Hi everyone, I am wondering if anyone has a recommendation for good tools out there that can predict whether two proteins will bind to one another. I know alphafold-multimer is state-of-the-art for this, but it is reliant on MSAs.

• I am specifically looking for tools excelling without MSAs.

Thanks!

Answer 1

[Mensur Dlakic]

I am specifically looking for tools excelling without MSAs.

I don't think there is such a tool that will excel at predicting protein interactions without MSAs. This is a challenging problem even with MSAs. However, the ESM family of models, specifically ESM3, might produce good multimer models without MSAs on a case-by-case basis.

https://github.com/evolutionaryscale/esm