Is there a way to guide your program to model a trimer instead of a "monomer"?
I have a 553 AA long protein which is assembled in a trimer. Obviously when I model it as a monomer it won't bear any usable results.
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Re: Modelling trimers
Currently, we just have a method for dimer modeling (https://zhanggroup.org/TACOS/). You can try to use Rosetta symmetry docking. You can also use Modeller if you have good trimer templates.