just take the murine dimer structure and superimpose two copies of your model on the two subunits by least-squares fit, e.g. in DeepView - Swiss-PdbViewer if you are already using it to interact Swiss model, in PyMOL or whatever other molecular viewer you are using. Since you have an asymmetric dimer, you might want to check whether there are conformational differences between the two monomer in the murine dimer. If so, you might also generate two models of the human sequence, using the two monomers in the murine dimer as template.

Hi, Annemarie H,

Thank you for your reply. Yes the monomer-monomer in mouse has a different conformation (i.e one of the monomer is bent as compared to the other monomer which is almost like a Y shaped structure), therefore i had difficulties doing it. I also tried using the sequence twice (funny) for modelling but it gave completely different results. I am now trying to modify the residues on mouse dimer (few of them to residues as seen in human sequence) but it is tedious. Therefore, was wondering if there is some other way of generating the dimer.

In this case you really have to make two models, one using monomer1 of the mouse structure as template, the second using monomer2. Download the mouse template structure and separate the two monomers into two files, then run swiss-model twice , choosing the option "user-provided template", once for each monomer in the mouse dimer.

Hi, Annemarie H,

Thank you again for the suggestion, in this case (modeling the individual monomers from the dimers separately) the question, next arises, is how to model them together then? When I am opening both the monomers, modeled this way, together in the Pymol, their arrangement appear like the Mouse Dimer; will this be a good model of human dimer protein?

If no, then, how will I get a good dimer structure (one bent and other straight, almost like a "Y") since I need to take it further for MDS?

Now you superimpose them individually on the corresponding subunits of the template dimer, just to make sure that their relative orientation has not changed in the modeling process. Look at the positions of your amino acid substitutions -at your level of similarity, I would not expect to see any major substitutions in the dimer interface. After making sure that the two chains of the model have different chain identifiers, you can combine them into a single pdb file.

Hii..

You can try SymmDock or Patchdock online tool for docking.

Ganesh: if you have a ~96% homology template for an asymmetric homodimer, the only reason to use docking to assemble the dimer is to test a docking tool!

Thank you Annemarie H, I have managed to make the dimer from the crystal structure.

Iqra Aroob

i directly used the template of the available dimer (from PDB) and did homology modelling (using Swiss Model tool) to build the structure & did energy minimisation and other fine-tuning (like loop modelling etc) to get the stable predicted structure.

Best

Hi.

Swiss modeller usually give you readymade dimeric structure. But what if you have to do this manually? I know there is a (pdb)matrix related trick to do so but I am not familiar with it.

I have a follow up question here- How can I identify the residue, critical for maintaining the dimer status of my protein from its crystal structure. I wish to introduce a mutation that will make my protein to exist (predominantly or always) as a monomer and carry out biochemical experiments. I have used PDBsum generate to find out several (many) residues involved in the interface of interaction. So many residues to screen by SDM is time consuming and I am in a hurry to quickly identify the critical residue.