In the context of the WestLife and BioExcel EU projects we have been working hard on a complete new design (and machinery) of our HADDOCK portal. The new version (HADDOCK2.4) does support cryo-EM data and will allow multibody docking up to 20 molecules.
We just published as a WestLife project deliverable a description of its implementation available in Zenodo (DOI:10.5281/zenodo.1252961).
We will soon be looking for beta testers to get feedback before putting it in production mode. So if you are interested, do contact us at software.csb_at_bonvinlab.org.