using antibody_graft

[croshong]

Hi My name is Jong hui Hong.

Recently I'm trying to graft cdr loops from one structure to another. while I'm trying to do that,

I found that rosetta has a command exactly for this purpose.

https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/antibodies/AntibodyCDRGrafter

https://docs.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-assemble-CDRs

But I could not find more detailed tutorial about this.

Can anybody give me some simple example about this command ?

Thanks

Regards

[croshong]

I could find some example in the rosetta source folder
main/tests/integration/tests/antibody_graft
It seems that FR.pdb in the folder is important
-s FR.pdb
-run::benchmark true # less optimization iterations in the stem optimiztion steps to make integration tests faster
-in:file:native ./LH_renumbered.pdb # native structure-
-antibody:h3_no_stem_graft true # graft the H3, but do not copy the stems from the templates, see details in documents
-check_cdr_chainbreaks false
FR.pdb file is similar to LH_renumbered.pdb .
Anybody know how to generate FR.pdb? Can I use LH_renumbered.pdb as a FR.pdb?

[roccomoretti]

A tutorial for the full RosettaAntibodyDesign protocol can be found at https://meilerlab.org/rosetta-antibody-workshop-2021/

To my understanding, the FR.pdb is simply the antibody framework onto which you're grafting the CDRs. I might be wrong, but the strange structure of FR.pdb in the test directory is simply to make it clear whether or not the grafting has worked. I believe (though I haven't fully tested) that you should be able to use a "normal" structure of the antibody onto which you're interested in grafting the loops. (That is, things will work if you use LH_renumbered.pdb instead of FR.pdb.)