Does the program support multiple antibodies in one complex?

[bzhousd]

Dear Authors,

Thank you for your great work.

Alphafold is able to take many chains, while I am not sure what format of input I should use for tfold-ag. for example I have chains like H(heavy chain) L (light chain) A(antigen) B(heavy chain), C(light chain), D( antigen).

so prot_ids.abag.txt will be
1PDB_H_L_A_B_C_D

and input msa file will have two msa in one a3m file, the order should be A and D, and separated by 0x00

Thanks

[wufandi]

Hi,
Thank you for your interest in our work. Unfortunately, tFold-Ag is currently unable to handle multi-chain antigen/multi-antibody input scenarios.
There is a method that might meet your needs:

1. Use tFold-Ag to predict 1PDB_H_L_A,
2. Use tFold-Ag to predict 1PDB_B_C_D.
3. Use AlphaFold to predict 1PDB_A_B.
4. Align the three complexes together based on A and B.

[bzhousd]

Thank you for your prompt reply. I have another question to ask. I wonder if tfold could output the equivalent pLDDT,

Thanks

[wufandi]

Yes, the plddt output by tFold-Ag is equivalent, but I would recommend you to judge the accuracy of the model prediction based on the ipTM score. It is highly correlated with the accuracy of the epitope.