Hi,
I want to use I-TASSER to model in a missing portion of my protein. I already have the structure of 2/3 of it, and I know what the structural homologs are. I have tried inputing my complete protein sequence with a homolog pdb as reference into the I-TASSER server, but the structure of the output model differs from the known portion of the protein and also fails to model in the missing part of the protein like the input homolog. Is there a way to tell I-TASSER how to assign secondary structure? These homologs have only been possible to identify after obtaining the portion of the structure that I have, so I'm concerned that general alignment and homolog searches are too inaccurate for this case. Any and all help is welcome! I'm at a loss for how to do this, but it seems possible.
Thanks!