Reuse MSA for multiple alphafold complex models?

Question

[Suicyte]

I am using a local installation of alphafold 2 for predicting the structures of two-protein complexes. Now, i plan to model complexes of a big protein A with many alternative (small) partners B1, B2, B3 etc. I seems a waste of CPU power to always re-do the extensive database searches for the A component. Is it possible to re-use the MSA folder (part A) generated in the first model for the subsequent models?

Answer 1

[massa.kassa.sc3na]

It appears that you may want to check out this pipeline https://github.com/KosinskiLab/AlphaPulldown.

(It does exactly what you are describing).