Are there journals for theoretical models of protein-protein interactions?
Protein-protein interactions is an area of biophysics, so certainly Biophysical Journal (published by Cell) is a nice place to look.

PNAS has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence.

The Journal of computational chemistry certainly about a lot of simulations and modeling, so see for yourself.

As for publications, the fact that you are asking for references makes me think you haven't done your homework on literature review, as it is always first and foremost job in a research project.