Re: [modeller_usage] how to build the loop of protein model using modeller

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 4/29/13 8:25 PM, aixintiankong wrote:
> i don't know how to build a model that  the protein, NAD+ and ligand
> coexsit and the loop of protein is disordered.

One way to do this would be to align your model sequence with the first 
template (loop is helix) for the entire sequence except the loop, and 
the second template (loop is disordered) for the loop:
http://salilab.org/modeller/9.11/FAQ.html#1

Another way would be to just use the first template, and just unalign 
the loop so Modeller builds it without template information:
http://salilab.org/modeller/9.11/FAQ.html#2

	Ben Webb, Modeller Caretaker
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