i have protein dimer sequences of chain A and B, how can i model these two sequences? i want to get as dimer. is there any software ? can you suggest?
I will show you a fast way to do it for presentation only,, but there will still be many errors in the structure model that you need to fix before it is in a good quality to design drugs or make studies on the structure.
you should first search the protein data bank (http://www.rcsb.org/pdb/home/home.do) just to check if there is known crystal structures of this portien. If not then you have to do homology modeling followed by protein-protein docking which is not a simple task.
Swiss Model server (https://swissmodel.expasy.org/interactive) can build a protein model for you depending on the closest known homolog tempelate structure. and sometimes there is no tempelate at all. remember that this model will likely have errors in protein backbone and side-chain rotamers in addition to atom-atom clashes. You will also need to add hydrogens to your protein (pdb files are without hydrogens to save space) and prepare protein for docking (minimization of energy is good approach).
After you get a model chain A and B ready for docking, you can use GRAMM-X server (http://vakser.compbio.ku.edu/resources/gramm/grammx/) to see alternative dimerizations of this protein.
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