Could HADDOCK be used to refine a docking complex made by HDOCK?
And if so, which refinement method would work best?
I am not familiar with HDOCK output, but in principle, if it’s a regular PDB file, then HADDOCK3 should be able to refine it. You can check input file requirements here: Haddock3 requirements - HADDOCK3 User Manual
And the choice of the module depends on the level of refinement you would like to apply: Refinement - HADDOCK3 User Manual
Typical choice would be flexref for the semi-flexible interface refinement. If you’re looking for a quick refinement to eliminate small clashes, then emref is better.
For only refinement purposes, I would recommend emref or mdref if you want a bit more flexibility.
The HADDOCK2.4 server also offers a refinement mode with different options.
Which one works better will depend on the quality of your initial conformation.
Check the following paper about refining complexes:
- T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4. Structure 30, 476-484 (2022).
Thanks, will do