Dear Sir,
I am trying to model a protein which has three domains seperated by linker
region in a linear fashion.Domain are not overlapping as they are
seperated by linkers.By macromolecular docking I generated their
best possible orientation and used as input PDB files.But the model given
by modeller wont preserve the provided orientation and domain got
seperated further by the linker regions.The template for linker region has
streches of helixes seperated by coils.
So what should I do to preserve the domain orientation and then generate
the possible model or I should use any other approach?
Waiting for your reply....
Research Student
Ranjit Kumar