Building A Dimer From No Template

Question

[Harpalss]

I have built a homology model for a monomer of a DNA protein. This protein is also known to dimerise. The dimerisation site had been identified.

What would be the easiest way to building a Dimer from the monomer I built taking the dimerisation site into account?

Answer 1

[Neilfws]

I'm reasonably sure that you cannot build a dimer by homology modeling unless you have a template (known structure) of a dimer. The dimerisation site alone is insufficient information.

See for example replies on the Modeller mailing list - reply 1, reply 2 and this information from SwissModel (scroll down to "Example: Modelling a dimeric protein").

If your protein is small and you have the resources (and know-how), molecular dynamics simulation might be an option. See for example How the hell do I model this thing by Bosco.