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TencentAI4S / tfold

open source code for Tencent tFold
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Does the program support multiple antibodies in one complex? #6

Open bzhousd opened 4 months ago

bzhousd commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

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

Thanks

wufandi commented 4 months ago

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.