Alphafold in colab - homotrimer

Question

[sjp24]

Hi, can anyone tell me please how do I view my protein as a homotrimer in colab alphafold. Do I just use a colon between the aa sequence and paste it three times? Thanks

Answer 1

[dthorbur]

Yes, you have it correct. Just add the sequence to a fasta delimiting the each chain with a colon.

example.fasta would look like:

>prot1_trimer
MQFPTSSTTEKTITEYVPWLYRFGQKLMPCQDNIPS:MQFPTSSTTEKTITEYVPWLYRFGQKLMPCQDNIPS:MQFPTSSTTEKTITEYVPWLYRFGQKLMPCQDNIPS

To view the prediction after, download the PBD if it's AF2 or the .cif file from AF3 and you can use software like PyMol and ChimeraX, or can use python libraries like MDanalysis for other downstream analysis of PDBs (I am unsure if that library can read .cif files).

[sjp24]

Thank you very much for replying. I did try this but I could only get it to work for one sequence, but that's OK, thanks again.

[dthorbur]

How odd. This works for me both on the colabfold notebook and on multiple instances of local colabfold that I have running at work. So long as the sequences aren't too long, can you add an examples fasta sequence and the commands you use try in your question?