[chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.

[Tan, Wei Ren]

Dear Sir/Mdm,

Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King's College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:

alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest)

Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?

Thank you very much and sorry to disturb you!

Sincerely Yours,
William Tan


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