Docking a protein with 6 domains

Hi, I have a protein containing 6 domains that are separated by a linker. The provided protein structure is linear (provided by alphafold).
Can I “change” the linear form of the protein for docking? The individual domains are fully flexible and I want to dock the protein around another protein at multiple sides (to wrap around the other).
However, the linear form only docks to one side.

I tried to mark the protein as fully flexible and to create a tbl file, but the 6-domain protein is still in linear form.

Thank you so much!


Hi Vanessa

This will be a challenging system to dock…

You would have to define restraints from the various binding site on the protein to your “disordered” peptide.

Defining it as fully flexible might not be enough.
You could try increasing the number of steps for the flexible refinement by e.g. a factor 5 or even 10 in this case (see the Advanced sampling parameter menu in the last submission tab of the 2.4 server) (does require guru access).

No warranty it will work though…

The alternative would be to cut your “linear protein” into pieces

I think the easiest way is then to cut my protein into pieces.

Thank you so much!