If you don't have crystal structure of the chemokines and cytokines , you can first generate a homology model. Then you can dock. However, docking is ideal for protein and small molecule. In this case, you can dock fragment of the protein. 

For autodock tutorial: https://www.youtube.com/watch?v=-GVZP0X0Tg8

For homology modeling: https://www.youtube.com/watch?v=XNqtBkpQCTQ

My question was, I have all the multiplex chemokine cytokines and ELISA data from serum. Then how can I model the interaction out of those 30 chemokine cytokines data. Are there any software or website for that?

I suspect this is what you're looking for ~ SAM analysis and network assessment, see this paper from Gary Nolan for citations:

Clinical recovery from surgery correlates with single-cell immune signatures

www.ScienceTranslationalMedicine.org 24 September 2014 Vol 6 Issue 255 255ra131