I have a question about modelling dimers. What I am trying to do is model
a homodimer. I have tried to few things that might work, but I am not
really sure. What I did:
1. Edited the pdb file for the template, making it all one subunit
2. My alignment file has the 60 amino acids from the first dimer
then chain of glycines then next 60 amino acids from the second dimer.
3. After I model, remove the chain of glycines and add back the B
domain letter to the pdb file.
The models look good. What does the group think? Will these models be
accurate? Will the restraints between the two dimers be included in the
models? Can I edit the restraints to remove the bad restraints located at
the end of the first dimer and beginning of the second?
Below is the alignment: I edited the 1a0a template change B domain to A and
adjusting the amino acid numbers.