Hi to everyone, I would like to get a feedback on the procedure I’m doing to possibly identify the binding interface between two proteins.
I have a ligand (~300 amino acids) and a receptor (~150 amino acids).
- First, I try to dock the amino acids 1-100 of the ligand with the receptor, than the amino acids 101-200 of the ligand with the receptor, and finally the amino acids 201-300 with the receptor (from these run usually I get a high restrain energy ~1000/3000).
- For any run i collect the best cluster according to the haddock score
- I determine the list of amino acids in contact between the three “best” clusters and the ligand
- I perform a new docking constraining the contact between the list of amino acids of the ligand and receptor I got from the step 3 (from these run I got a lower restrain energy, but still high ~200/400)
- eventually re-determine the list of amino acids in contact from the best cluster and re-run the docking using the new list
My questions are:
- Does this scheme make sense according to the way haddock works?
- Are the final value of the restrain energy reasonable or still too high?
- which force field is used to compute the energy terms of the molecular complex? (I would run a gromacs simulation to check the stability of the “best” complex I get at the end)
Thanks for any help, and happy new year