I am new to haddock and am looking to model the interactions of an adenovirus fibre-knob domain (a homotrimer; PDB 6HCN) with three receptors from non-human species (three identical CAR receptors) that I have used AlphaFold2 to make. The receptors normally dock on each of the trimers in the fibre knob. I can’t figure out how to dock with all three CAR molecules at once - is there a way to do this?
The other concern I have is that I was planning on performing the docking as per the tutorial “HADDOCK2.4 tutorial for the use of template-derived pairwise distance restraints to guide docking”, however there seems to be a problem with the PS-HomPPI2 server as it is not providing any results (with the tutorial data and also with mine). Is there another way you would recommend producing a .tbl file?
I am new to haddock and am looking to model the interactions of an adenovirus fibre-knob domain (a homotrimer; PDB 6HCN) with three receptors from non-human species (three identical CAR receptors) that I have used AlphaFold2 to make. The receptors normally dock on each of the trimers in the fibre knob. I can’t figure out how to dock with all three CAR molecules at once - is there a way to do this?
In principle yes - would be a four body docking with C3 symmetry between the CAR molecules.
But simpler to only dock one CAR to one interface and later one build the trimer by symmetry.
The other concern I have is that I was planning on performing the docking as per the tutorial “HADDOCK2.4 tutorial for the use of template-derived pairwise distance restraints to guide docking”, however there seems to be a problem with the PS-HomPPI2 server as it is not providing any results (with the tutorial data and also with mine). Is there another way you would recommend producing a .tbl file?