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Re: [modeller_usage] Homology modelling a loop



On 2/24/15 12:14 PM, Anjela Manandhar wrote:
I need to model a missing loop for my protein. I used the sequence of
missing loop and aligned with its homologous sequence. Then I modeled my
loop from the alignment. Now the problem is my modeled loop is very far
away from the place where it needs to be ( due to the template i used).
So how can I stitch my loop into the protein. Also, is there a way to
homology model the loop such that its position is within the protein.
I am attaching my script and alignment files.

The best solution would be to include both templates in your alignment. Make sure there's some overlap between the two templates at the ends of the loop.

	Ben Webb, Modeller Caretaker
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