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HWaymentSteele / AF_Cluster

Predict multiple protein conformations using sequence clustering and AlphaFold2.
MIT License
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Example for generating initial MSA input #4

Closed ackbar03 closed 2 years ago

ackbar03 commented 2 years ago

Hi,

Thanks for providing your code!

Can I ask what is the easiest way to generate the additional MSA input for clustering? I see that you guys mention in the paper you used the ColabFold implementation of MMSeq. I see there is a search.py file under :

https://github.com/sokrypton/ColabFold/blob/main/colabfold/mmseqs/search.py

Should I run this to generate my MSA's?

Thanks!

ackbar03 commented 2 years ago

Oh actually I just saw this.

https://colabfold.mmseqs.com/

I'm guessing this was what was used?

HWaymentSteele commented 2 years ago

Hello! For all the constructs in the biorxiv preprint, the MSAs were generated using the AlphaFold notebook at https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb. This calls the same code as those other resources.