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Question: How can I obtain ~same speed as the server ? #233
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Same problem! |
Please check the following computational environment:
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Hi! I need to fold around ~1k dimers and I was wondering whether it is faster to download MMseqs2 locally (colabfold_search) or use the MSA server (colabfold_batch). If so, how much faster? Also, many of these dimers share the same monomer. Is there a way of speeding things up knowing that? |
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Hello,
First of all thank you for sharing your work!
I tried to install and use colabfold locally, and use colabfold_search instead of the server (I have ~7000 proteins to predict). I managed to use it, and mobilised the required ressources (1tb ram, performant CPU etc), but I still can't manage to obtain the .a3m files with a correct speed. It takes ~1h per protein. I used this tutorial https://qiita.com/Ag_smith/items/bfcf94e701f1e6a2aa90 as an example for my code.
Could I see more examples of how do you run colabfold_search, especially for a folder full of fasta files?
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