I would like to dock Insulin with another protein/receptor. I am considering the 51 aa long Insulin protein with two chains (A:21 and B:30). What would you suggest in this regard?
Use the dimer, but make sure that there is no overlap in numbering between the two chains since HADDOCK will treat it as one molecule
I renumbered the residue numbers. Would you suggest I do the same with the atom numbers as well over PDB ?
On renumbering the residues, I got a PDB with a long linear chain connecting the two chains.
Atom numbers are not important
And you can keep the TER statement between to the chains.
It the termini are anyway not close haddock will detect a chain break
I kept the TER statement between the two chains and renumbered the residues and changed the chain identifier to a single chain. The input file for the Insulin shows no linear linker between the two chains but the output showed the same linker which I was trying to avoid.
I set up another docking with no change in chain identifiers,but then again the output file shows a linker between the two chains which I wanted to do away with! Any suggestions ?
I kept the TER statement between the two chains and renumbered the residues and changed the chain identifier to a single chain. The input file for the Insulin shows no linear linker between the two chains but the output showed the same linker which I was trying to avoid.
This is only a visualisation problem…
And I should just remove the linker in between?
Are you sure there is a linker in between…?
It is again probably simply a visualisation artefact. The generated PDB does not have the TER statement, but it does not mean there is a peptide bond created!
You can calculate the distance between the N and C atoms to see if there is really a peptide bond defined.