I originally posted my question regarding modeling of a multi-domain oligomer under a different thread. After getting a lot of useful answers and consulting Ingemar Andre off the list I am still facing one major problem.
The protein at hand consists of two domains A and B connected by a structured linker. Structural models for all three "parts" are available. How would one connect these to obtain a full-length model?
This refers specifically to Ingemar's and Rocco's following advise for obtaining a oligomeric structure of my protein:
1) Make the domainA-linker-domainB model(s).
2) Symmetrically dock the model(s)
1) Separately dock domainA and domainB
2) From a set of decent looking models from self-docking with domain A and domain B find combinations of dimers of A and B that would be able to connect with a linker.
3) Place the domains in such a manner that a linker can connect A to B.
4) Connect the linker to the proteins using loop modeling to close the covalent links between A, linker and B.
Thanks once more in advance.