Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template pdb_id
The modelled structure does not have constant portion of the antibody.
Category:
Post Situation:
Generally speaking, Rosetta modeling tends to work with the Fv region of the protein -- for most modeling problems that's the region of the structure which is actually "interesting".
If you do happen to need a model of the full Fab or full antibody structure, my recommendation would be to look into combining the modeled Fv region with a known model of the rest of the antibody. Using something like RosettaCM, you can use multi-template "homology modeling" combine the two structural models. (The modeled Fv region is used as a template for just the variable region, and your constant region model is used for the template of the rest.) So long as there's a small amount of overlap (e.g. keep just the first bit of the Fv in your constant region model), RosettaCM should be able to graft the two models together.