hi,
I've been using i-Tasser "TM-align" to align two crystal structures, let's say CS-A and CS-B. This worked very well and the alignment score based on CS-A was 0.86 and for CS-B was 0.73.
Protein B is a hexamer made up of 3 dimers, and the crystal structure of B was solved as a hexamer.
Protein A is a dimer, and was crystallized as a dimer. Based on the high level of structural similarity, I wanted to test if protein A could also form a hexamer made up of 3 dimers.
Is there a mechanism to model protein A into the protein B hexamer? Is this something that should be done using different software such as Schrodinger? (and if so, could you recommend a website with instructions?).
Many thanks for ideas.