Reuse MSA for multiple alphafold complex models?
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?
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Suicyte •
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It appears that you may want to check out this pipeline https://github.com/KosinskiLab/AlphaPulldown.
(It does exactly what you are describing).
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