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?