I have been using CLUSPro 2.0 for protein-protein docking, but it does not take the metal ion into consideration because it selectively takes the protein chain. In contrast, HADDOCK considers the metal ion but i can only able to fed the monomoric protein bound with ion to the monomeric target receptors. How can i rectify the issue.Is it feasible to consider the dimeric target protein as a single entity, if so HOW???
Well, you can trick most programs into accepting a multi-chain protein (homo- or hetero-oligomer) as a single chain protein by first making sure that each amino acid has an unique residue number and then setting all to the same chain ID:
e.g. for a dimer with 100 residues in each chain (chain A and B), set the residue numbers to 1-100 for chain A, 101-200 for chain B, then set the chain ID to A for all residues.
You can do this using the "alter" command in PyMOL https://pymolwiki.org/index.php?title=Alter&redirect=no
alter (chain B), resi=str(int(resi)+100)
alter (chain B), chain="A"
The only problem with this approach is that the C-term of chain A and the N-term of chain B will not be treated as proper charged termini, but rather as a chain break due to unresolved residues. Therefore in the immediate vicinity of these termini, the electrostatics will be off, and these termini will not be able to form the appropriate hydrogen bonds, therefore docking solutions involving this region will be suspect.
Yes, you can dock multichain protein in HADDOCK.
They have given protocol in PDBTOOLS https://wenmr.science.uu.nl/pdbtools/
Follow the given steps and prepare files accordingly. Be sure each chain has unique chain IDs.