I have two proteins as restraint and then predict the N-terminal of one protein which interact the other protein. Which protocol I should use?
Thanks in advance
You can try FloppyTail protocol.
Your question is a little vague - what exactly do you have? Do you have structures of two proteins, which bind to each other through an N-terminal region of one not present in its structure?
The FloppyTail protocol is intended for sampling space of flexible tail regions, including those which bind some other partner.