I performed tertiary structure prediction of my enzyme in Modeller. However, it is predicted to be a homodimer. How can I obtain a homodimer from the monomer obtained by prediction in a reliable way?
It is not a protein modeling task anymore, but rather a problem of protein-protein interactions. There are a few public servers for protein-protein docking, such as HADDOCK (http://milou.science.uu.nl/) or Rosie (https://rosie.rosettacommons.org/docking2). It must be kept in mind though, that these docking models are very hypothetic (even more hypothetic than 3D protein models built from their sequences).