Hi, sorry for once again for bothering , I am now interested in docking the HLA-E nonamer peptide , VMAPRTLFL, with the receptor proteins of NKG2A/CD94. Is it wise to have the docking parameters setup as mentioned in https://www.bonvinlab.org/education/HADDOCK-binding-sites/#ab-initio-surface-based-docking-with-haddock ?
Also , shall I Fix molecule at its original position during it0 for the receptor protein?
And you have no knowledge of the binding site on the receptor side?
This seems a MHC-like receptor and usually the binding of peptide occurs through well defined anchor residues (positions 2 and 7 in the peptide).
The ligand binding site tutorial does not make sense in this case
For my knowledge , yes the peptide on position 2and 7 are anchor to MHC molecules while position 5, 6, and 8 will involve in the interaction with the receptor protein. So in this case, i shall specific the active residue of peptide to be 5, 6 and 8 ?
In principle yes, but the peptide will not be recognized on its own but in the context of the MHC molecule - so you should model the full thing
Noted with thanks, prof. Let’s say if i just wanna dock the peptide with NKG2A/CD94, will AutoDock Vina be a more suitable tool compared to HADDOCK due to difference in algorithm ?
Whatever works best for you…
In HADDOCK you can define restraints to target the docking.