I'm a newcomer to the field of antibodies, and I'm seeking guidance on obtaining 3D structures for my molecular simulations. After browsing the PDB databank, I noticed that there are Fab and Fc structures available. My specific interest lies in investigating the structural dynamics in the entire antibody (AB) and on the hinge region.
I have a few questions:
Is it common practice to attempt building the entire antibody structure and hinge regions from PDB files for fragments, or are there recommended alternatives?
Are there comprehensive PDB structures available for different IgG and therapeutic antibodies that include information on the whole structure and hinge regions? Especially for Bevacizumab and Rituximab?
Does it make sense to select single segments, e.g., CH1, VH, VL, for analysis? Would one expect these structures to be reasonably stable?
Additionally, I'd appreciate any insights into common pitfalls and any recommendations you might have for someone new to this field.
Thank you in advance for your time and assistance.
Best regards, Albert