How to use ColabFold to predict the 3D structure of a protein dimer linked by a disulfide bridge?

Hi,

I am attempting to utilize ColabFold to predict the 3D structure of a protein dimer connected by a disulfide bridge.

I understand that AlphaFold can accomplish this using the following command line:

alphafold_run(
    fasta_file="protein_dimer.fasta",
    disulfide_bond_connectivity="C100-C200",
    homology_models=["protein_dimer_homology_model.pdb"],
    experimental_data=["protein_dimer_cryo_em.mrc"],
    temperature=0.5,
    num_iterations=100
)

However, I lack the necessary resources to execute AlphaFold on our GPU cluster.

Fortunately, I have learned that ColabFold is capable of performing this type of analysis.

Unfortunately, I have been unable to determine how to input the parameters required for such an analysis.

I would greatly appreciate your assistance and guidance.

Thank you for your time and consideration.

Best,

Alexis

Start by reviewing ColabFold's documented input options and the parameters listed in the issue, including disulfide connectivity, homology models, experimental data, temperature, and iterations. Confirm whether ColabFold supports these inputs and document the supported workflow or limitations; done means the requester has clear guidance for running the dimer prediction.