Bad question, try to be more specific: - what kind of network? (regulatory?), - you mean -re-contstruct, right, if it's constructing, just go ahead - docking domains (do you mean protein-docking?, confused with transcription factor binding site?) - which plant?

I would also recommend you to re-read the answer(s) provided by biostar members for your first question Do You Know Of Any Tools For Inference Of Docking Sites In Plants? . If some aspects are not clear, you may add comments to respective answers.

Given eminencegrise history of never posting very specific questions and not adding anything sensible, I doubt op will do something. These questions sound more like: I'm trying [?]. with tool [?] can you point me to.... and you get ... a question bot.

I meant reconstruct as there are sections that are known,I am using 23 species, that is why I was asking regarding a database for plants, protein docking, NOT TF binding sites, and I thought more general will apply to more people rather than providing details yet knowing Your opinions I will surely increase the level of details,

and I meant knowledge relying approaches NOT de novo

Ok, added the protein-protein-interaction tag, if that is what you meant? I don't know almost anything about PPI/docking, and I do not fully understand what type of network you are trying to reconstruct. Anyway, googling "protein docking arabidopsis" found this: "AtPIN: Arabidopsis thaliana Protein Interaction Network" [http://www.ncbi.nlm.nih.gov/pubmed/20043823]. It's not a real answer, but it maybe takes you closer?