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Re: [modeller_usage] request a clear method for modelling a dimeric protein

On 10/07/2009 02:05 AM, Othman Houcemeddine wrote:
I am trying to use modeller to predict the structure of a dimeric
protein with no obvious symmetry between each of its subunits. My BLAST
search shows that the first subunit alpha is homologous to a monomeric
protein "C", while the other subunit beta is homologous to another
different monomeric protein "D". Basically, I tried to align alpha with
"C" and beta with "D" and I decided that the best strategy is to use a
typical script from the tutorial"Building a model from multiple templates".
I am not quite sure that this procedure is the best way to build my
model. Also, I found a problem in writing my alignment file especially
the header section and the assignment of each of the subunits to each of
the templates.

Sounds fine. But what was the problem that you ran into?

Could any body verify my alignment file and give me a clear method to
deal with this situation?
Alignment file.ali:
structureX:C: 1:A:58: : : : :
structureX: D:1:A:78:::::

Your script and alignment look fine to me. But since there is no overlap between your two templates, the two chains in your output structure will probably not be correctly oriented.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage