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

[sabrina23]

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 Retro Bowl 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

To use DeepMSA output in ColabFold or AlphaFold, you need to format the output into the required MSA format, typically `.fasta` or `.aln`. For ColabFold, separate MSAs for paired sequences and individual sequences are needed, while AlphaFold can directly accept custom MSAs.