Homology modelling a loop
Hello, 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. Sincerely, Anjela Manandhar Graduate Student Biochemistry Program Graduate Center, City University of New York 365 Fifth Avenue, NY-10016, USA
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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Anjela Manandhar -
Modeller Caretaker