I want to model a dimer of a two domain (A and B) protein. The x-ray structures of the homodimers of the two domains (A1+A2 and B1+B2) are known, and there's a superposition of residues from the two structures. However, if I superpose this common interval of residues two connect the domains A1 and B1, A2 and B2 will not be connected, which is expectable, as the domain linker is supposed to be flexible. What I want to do, so, is a model job which considers the four domains and their dimerization interfaces as almost rigid, but let the linker region be flexible in order to connect them properly. How could I do such a task?
Lucas
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