Hey, I am trying to dock 5 proteins (1 main + 4 small proteins) with each other to create a protein scaffold, but the parameter page keeps getting reloaded and not showing any error (I am using the web portal). Could you please tell me how to dock multiple proteins using HADDOCK software?
Dear user,
On the web-portal, to perform multi-body docking, you may not find all the tool required to properly set the restraints.
Indeed, the combinations of active and passive residues selection is made from a matrix of pairs, and you cannot directly define interactions between two entities only (this is not a problem when performing two body docking).
To be able to properly define those restraints, I would strongly recommend using the haddock-restraints tool (web server accessible here: https://wenmr.science.uu.nl/haddock-restraints).
Over there, you can better attribute pair of restraints by nicely defining the partners to be involved.
You can generate and download the corresponding restraints and then input them on the HADDOCK web-portal.
For this, you will need to have expert/guru account level, something you can ask for in the user dashboard -> request elevated permissions.