Dear my modellers:
I am modeling a chimeric protein from two different proteins, which have known structures. There is no overlap between them,so i oriented two domains before the modeling. But i got an unreasonable model in which one domain so called 'lid' was just beside the other catalytic domain,even under some distance restraints to some reference residues i used. It is believed that hydrophobic interaction drives two domains forming a closed conformation. So,should i use something like hydrophobic restraints to the modeling, and how to do this?
Thanking you in advance.