Zhanglab forum

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

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

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

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.