Reply To: How to dock 3 missing domains onto a multi-domain protein

[Anonymous]

This is a very complex problem. There is no single command line to do something like this. Experimental constraints are going to be useful, do you have any?

I would start with docking B and E individually to the main+CD complex. If you get a good funnel on either of those (or if you have experimental constraints), try loop modeling to see if the B or E placement allows for a reasonable loop. Iterate through this, adding one more domain at a time.

You could hack the FloppyTail code a bit to get it to treat the B-C or D-E loop as a tail, then place the B or E domain as a big rigid chunk on the end of the tail, to try to sample what orientations B or E might land in (then iterate out to A). I think docking is superior here.