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?
1 answer
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.
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