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question about antibody modeling and snugdock process option

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question about antibody modeling and snugdock process option

I am currently working on a simple test with antibodies.

I have a question in this regard, can I use deepab instead of rosetta antibody to create antibody structures? When I looked at the snugdock paper, it seems that there is an additional protocol when using a tool other than rosetta antibody, but I know that deepab creates structures based on rosetta. So I am wondering if I can proceed in the same way as rosetta antibody when using deepab. 

And I plan to superimpose the generated antibody and antigen to the original pdb to overlap, then prepack and snugdock.

Is there anything wrong with this process? I was wondering if the H3 modeling is a necessary part of it.

Also, one more question,  

Since I need to run multiple tests, I'm also thinking of docking only the heavy chains considering the computing power, is it a problem to proceed this way?
In the paper on snugdock performance validation, it says that only heavy chains can be used, but I was wondering if this is only for nanobodies or if this is an option for antibodies as well.

And if it is, I would like to know how to use only heavy chains!


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Sun, 2023-04-16 19:18