I want to construct the structure of a hetero dimer protein. How can I do that?
Do you have the the AA sequence of the protein you want to construct the structure? If yes, given an amino acid sequence, you can find which protein(s) of known 3-D structure are similar to it. Use BLAST against the PDB database to find templates. Then you choose a template based on the alignment, more similarities etc. It is important to have a good alignment. Then you create your model using a homology modelling software (i.e http://salilab.org/modeller/). Then you refine your model and finally you evaluate it (you can use http://swift.cmbi.ru.nl/servers/html/index.html, https://prosa.services.came.sbg.ac.at/prosa.php etc ).
Assuming you already have two monomeric proteins, you can dock them using HADDOCK (automation) or Xplor-NIH (manual).
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