Use DeepMSA2 output in ColabFold or AlphaFold

[Qiping]

Dear DMFold authors,

Thank you very much for the very useful tool. I am trying to use DeepMSA output as the input into ColabFold, but ColabFold needs MSA for both paired sequences and the two sequences alone. May I ask how I can derive the desired format from DeepMSA output? If DeepMSA can work with AlphaFold, I am also happy to learn how to put DeepMSA output into AlphaFold. Meanwhile, if DMFold itself can accept custom MSAs and templates, I am also eager to learn how to use it because I have many similar sequences - whose MSAs and templates can be the same - to predict structure from. Any help or guidance is highly appreciated!

Thanks!
Qiping

[jlspzw]

Dear user,

DeepMSA2 and DMFold can output paired MSA and single MSAs. you can find one example in DMFold example folder
example/AF2Models/aMSA-aMSA/multi2.2-v4/seq/msas/paired.aln and example/AF2Models/aMSA-aMSA/multi2.2-v4/seq/msas/A

DMFold itself accepts customs MSAs, and you can check details at DMFold/bin/alphafold_multimer/run_alphafold_mymsa.sh

Let us know if you have any questions.

Best Regards
Wei Zheng

[thiery]

I’ll definitely keep those DeepMSA2 to AlphaFold steps in mind when I’m geometry dash apkworking on MSA inputs next time.

[Harry25]

That’s an interesting question, and I can see how working with different tools like DeepMSA, ColabFold, and AlphaFold can get a bit tricky when formats don’t match directly. It kind of reminds me of when I first tried experimenting with creative apps outside of my usual workflow—like stumbling across the Incredibox mod APK latest , which gave me a new way to play around with sounds I was already familiar with. Sometimes the right format or tool makes all the difference, and I hope you find a smooth way to connect DeepMSA with ColabFold or AlphaFold for your project.