Help understanding HADDOCK's different refinement methods

HADDOCK
1

Hi all. I got this result from AlphaFold2 for a heterotrimer, and I want to check out different binding options using the ‘refinement’ method. I see the interface gives me four different choices: ‘water refinement (default)’, ‘coarse grained refinement’, ‘energy minimization refinement’, and ‘simulated annealing with centroid restraint’.

I tried the water refinement and it gave me a bunch of useful binding alternatives, but the ‘simulated annealing with centroid restraint’ option only gave me back a single structure.

Could someone give me some info about this ‘refinement’ method? I’ll take any information I can get. Thanks!

2

If you just want to refine your complex, the default protocol is best.
It does perform a very short MD in water and does generate several models.

For more details of the various protocols (in the context of refining low/medium resolution EM models) check the following paper:

3

Thank you very much Dr. Bonvin!