Requesting feature: ability to skip MSA generation step

[swanss]

Hi,

I'm currently running the example and everything seems to be going smoothly. I'm interested in using this in pulldown mode, where I have a natural protein and a list of peptides which are designed or otherwise synthetic. As the peptides have no homolog there is little reason to spend time generating MSAs for each. Would it be possible to control for which proteins the HMM search is performed during feature generation? I'm not sure whether it would be easier to create dummy MSA files (which are empty) or to just modify the run_multimer_jobs.py to handle the case where a peptide has no MSA, but either would work fine for me.

Respectfully, Sebastian

[dingquanyu]

Hi Sebastian,

Many thanks for your interests in our package and it's a very helpful suggestion. We're actually working on scripts that can skip MSA steps in another programme and will add this feature to AlphaPulldown as well in the future.

Yours, Dingquan